@fideus-labs/ngff-zarr 0.2.8 → 0.4.0

package/esm/utils/compute_omero.js

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+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Compute OMERO metadata from NgffImage data.
+ */
+import * as zarr from "zarrita";
+/**
+ * Glasbey color palette from colorcet's glasbey_hv.
+ * Extended from HoloViews default colors using the Glasbey algorithm
+ * for maximum distinguishability across 256 categorical colors.
+ * See: https://colorcet.holoviz.org/user_guide/Categorical.html
+ */
+export const GLASBEY_COLORS = [
+    "30A2DA",
+    "FC4F30",
+    "E5AE38",
+    "6D904F",
+    "8B8B8B",
+    "17BECF",
+    "9467BD",
+    "D62728",
+    "1F77B4",
+    "E377C2",
+    "8C564B",
+    "BCBD22",
+    "3A0183",
+    "004300",
+    "0FFFA9",
+    "5E0040",
+    "C6BDFF",
+    "425052",
+    "B80080",
+    "FFB7B3",
+    "7D0200",
+    "6126FF",
+    "FFFF9A",
+    "AEC9AB",
+    "00867C",
+    "553A00",
+    "94FCFF",
+    "00BF00",
+    "7D00A0",
+    "AB7200",
+    "91FF00",
+    "01BE8A",
+    "00457B",
+    "C8826F",
+    "FF1F83",
+    "DD00FF",
+    "057400",
+    "644461",
+    "888FFF",
+    "FFB6F4",
+    "536237",
+    "CE85FF",
+    "686A84",
+    "BEB4BE",
+    "A56089",
+    "95D3FF",
+    "0100F8",
+    "FF8002",
+    "8B2945",
+    "ADA06D",
+    "53458B",
+    "C8FFD9",
+    "AA4600",
+    "FF798F",
+    "83D371",
+    "909EBF",
+    "9400F5",
+    "EBD09B",
+    "AD8BB1",
+    "00634A",
+    "FFDC00",
+    "887751",
+    "7EABA3",
+    "000097",
+    "F500C6",
+    "653329",
+    "006678",
+    "04E3C8",
+    "A737AE",
+    "C5DBE1",
+    "4D6EFF",
+    "9B9301",
+    "CD586B",
+    "EFDEFE",
+    "795A00",
+    "5F889A",
+    "B4FF92",
+    "5E726B",
+    "520066",
+    "058751",
+    "84206F",
+    "3C9605",
+    "657300",
+    "F1A06C",
+    "5F5045",
+    "BD004A",
+    "D06827",
+    "D796AB",
+    "895DFF",
+    "826C76",
+    "2B55B9",
+    "6E7CBB",
+    "E7D5D3",
+    "5D0018",
+    "7C3B01",
+    "80B17D",
+    "C8D97D",
+    "00E83B",
+    "7CB2FF",
+    "FF55FF",
+    "A42721",
+    "1DE4FF",
+    "7DAF3B",
+    "7B4B91",
+    "E0FF48",
+    "6B00C4",
+    "CDA897",
+    "BE63C4",
+    "89CDCE",
+    "4603C8",
+    "5E9279",
+    "414A01",
+    "05A79D",
+    "CF8C37",
+    "FFF8D0",
+    "435471",
+    "B544FF",
+    "CF4993",
+    "CFA4DF",
+    "94D400",
+    "A794DA",
+    "2DA558",
+    "8DE3B6",
+    "A4A99D",
+    "6C5CB7",
+    "FF7E5E",
+    "A7838A",
+    "AFBED8",
+    "2AC4FF",
+    "A6683D",
+    "F691FE",
+    "874B64",
+    "FF0C4B",
+    "215E23",
+    "4292FF",
+    "87839D",
+    "672D45",
+    "B14F41",
+    "004E53",
+    "5F1B00",
+    "AD4167",
+    "503267",
+    "D6FFFD",
+    "7FB5D1",
+    "A9B969",
+    "FF96CB",
+    "C87495",
+    "365039",
+    "FFD063",
+    "5E5862",
+    "879476",
+    "A978FF",
+    "03C863",
+    "E7BED4",
+    "D4E3D0",
+    "876790",
+    "897C27",
+    "CDDCFF",
+    "AA676B",
+    "323474",
+    "FF5EA9",
+    "009BB0",
+    "71FFDD",
+    "785C38",
+    "50659B",
+    "CC00B3",
+    "577B55",
+    "516E7B",
+    "015F92",
+    "AABDBE",
+    "017F99",
+    "04DD97",
+    "873A2C",
+    "F0968E",
+    "75C6AA",
+    "70695D",
+    "CCDC09",
+    "AF8557",
+    "D80075",
+    "9D3F81",
+    "D94500",
+    "DD6754",
+    "5FFF79",
+    "D5B173",
+    "62265E",
+    "BAA23D",
+    "D9F2B3",
+    "57028F",
+    "A19BAA",
+    "4D4A27",
+    "A4A9FF",
+    "ACE8DB",
+    "995901",
+    "AC00E2",
+    "47822F",
+    "CBC3AD",
+    "00C5B6",
+    "615378",
+    "336D68",
+    "A59280",
+    "8499A2",
+    "FD5764",
+    "7096D2",
+    "728D07",
+    "7F004C",
+    "1530A0",
+    "D1C1E2",
+    "C985D0",
+    "6C454B",
+    "7F0024",
+    "00A279",
+    "B2A9CF",
+    "F90000",
+    "B0E9FF",
+    "939E50",
+    "727A82",
+    "D92E55",
+    "476101",
+    "0059FF",
+    "7740B5",
+    "ACE460",
+    "674525",
+    "525D51",
+    "957368",
+    "A9E49A",
+    "A30058",
+    "D962F6",
+    "8E7DCF",
+    "FFBD93",
+    "A30092",
+    "9AFFB9",
+    "A7C2FF",
+    "F46200",
+    "E5F0FF",
+    "B89CA4",
+    "609694",
+    "FF9F35",
+    "8C2900",
+    "726B32",
+    "DF824E",
+    "AF7BD5",
+    "BC2D00",
+    "7B6FA3",
+    "484362",
+    "C7A3FF",
+    "004D28",
+    "C4C68E",
+    "E048D7",
+    "E7E965",
+    "E5C10B",
+    "00F4F1",
+    "9F5BA2",
+    "4C41B7",
+    "65338E",
+    "767E6C",
+    "A98A36",
+];
+/**
+ * Get default colors for channels.
+ *
+ * For a single channel, returns white (FFFFFF).
+ * For multiple channels, uses the Glasbey color progression.
+ */
+export function getDefaultColors(nChannels) {
+    if (nChannels === 1) {
+        return ["FFFFFF"];
+    }
+    // Cycle through Glasbey colors if we have more channels than colors
+    return Array.from({ length: nChannels }, (_, i) => GLASBEY_COLORS[i % GLASBEY_COLORS.length]);
+}
+/**
+ * Validate that quantiles are in valid range and properly ordered.
+ */
+function validateQuantiles(quantiles) {
+    const [low, high] = quantiles;
+    if (!(low >= 0.0 && low <= 1.0)) {
+        throw new Error(`Low quantile must be between 0 and 1, got ${low}`);
+    }
+    if (!(high >= 0.0 && high <= 1.0)) {
+        throw new Error(`High quantile must be between 0 and 1, got ${high}`);
+    }
+    if (low >= high) {
+        throw new Error(`Low quantile must be less than high quantile, got (${low}, ${high})`);
+    }
+}
+/**
+ * Validate that a color is a valid 6-digit hexadecimal string.
+ */
+function validateColor(color) {
+    const hexPattern = /^[0-9A-Fa-f]{6}$/;
+    if (!hexPattern.test(color)) {
+        throw new Error(`Color must be a 6-digit hexadecimal string without # prefix, got '${color}'`);
+    }
+}
+/**
+ * Maximum sample size for approximate quantile computation.
+ * For datasets larger than this, we use reservoir sampling for memory efficiency.
+ */
+const QUANTILE_SAMPLE_SIZE = 10_000;
+/**
+ * Helper function to compute quantile from a sorted array.
+ */
+function computeQuantile(sortedValues, q) {
+    if (sortedValues.length === 0) {
+        return NaN;
+    }
+    if (sortedValues.length === 1) {
+        return sortedValues[0];
+    }
+    const index = q * (sortedValues.length - 1);
+    const lower = Math.floor(index);
+    const upper = Math.ceil(index);
+    const weight = index - lower;
+    if (lower === upper) {
+        return sortedValues[lower];
+    }
+    return sortedValues[lower] * (1 - weight) + sortedValues[upper] * weight;
+}
+/**
+ * Compute channel statistics (min, max, and quantiles) from array data.
+ *
+ * For large datasets (>10,000 non-NaN values), uses reservoir sampling
+ * to compute approximate quantiles with reduced memory footprint.
+ * Min and max are always exact.
+ */
+function computeChannelStatistics(data, quantiles) {
+    let min = Number.POSITIVE_INFINITY;
+    let max = Number.NEGATIVE_INFINITY;
+    // Reservoir sample for approximate quantile computation
+    const sample = [];
+    let count = 0;
+    for (let i = 0; i < data.length; i++) {
+        const v = data[i];
+        if (Number.isNaN(v)) {
+            continue;
+        }
+        // Update min and max (always exact)
+        if (v < min)
+            min = v;
+        if (v > max)
+            max = v;
+        // Update reservoir sample for quantiles
+        if (sample.length < QUANTILE_SAMPLE_SIZE) {
+            sample.push(v);
+        }
+        else {
+            // Reservoir sampling: replace random element with probability QUANTILE_SAMPLE_SIZE/(count+1)
+            const j = Math.floor(Math.random() * (count + 1));
+            if (j < QUANTILE_SAMPLE_SIZE) {
+                sample[j] = v;
+            }
+        }
+        count++;
+    }
+    if (count === 0) {
+        return { min: NaN, max: NaN, qLow: NaN, qHigh: NaN };
+    }
+    // Sort sample for quantile computation
+    sample.sort((a, b) => a - b);
+    const qLow = computeQuantile(sample, quantiles[0]);
+    const qHigh = computeQuantile(sample, quantiles[1]);
+    return { min, max, qLow, qHigh };
+}
+/**
+ * Extract a single channel from multi-dimensional typed array data.
+ */
+function extractChannel(data, shape, channelIndex, channelDimIndex) {
+    const nChannels = shape[channelDimIndex];
+    const result = [];
+    // Calculate the stride for the channel dimension
+    let channelStride = 1;
+    for (let i = channelDimIndex + 1; i < shape.length; i++) {
+        channelStride *= shape[i];
+    }
+    // Calculate the total size of dimensions before the channel dimension
+    let outerSize = 1;
+    for (let i = 0; i < channelDimIndex; i++) {
+        outerSize *= shape[i];
+    }
+    // Extract all values for this channel
+    for (let outer = 0; outer < outerSize; outer++) {
+        const outerOffset = outer * nChannels * channelStride;
+        const channelOffset = outerOffset + channelIndex * channelStride;
+        for (let inner = 0; inner < channelStride; inner++) {
+            result.push(data[channelOffset + inner]);
+        }
+    }
+    return result;
+}
+/**
+ * Compute OMERO metadata from an NgffImage.
+ *
+ * This function computes visualization parameters (OMERO metadata) from image data:
+ * - min/max: The actual data range
+ * - start/end: Display window based on quantiles (default 2% and 98%)
+ *
+ * For multi-channel images (with 'c' dimension), statistics are computed
+ * separately for each channel, resulting in per-channel OMERO windows.
+ *
+ * Memory requirements: This function loads the entire image data into memory
+ * for statistics computation. For large images, use the lowest resolution
+ * image from a multiscales pyramid.
+ *
+ * Edge cases:
+ * - If all values in a channel are NaN, the statistics will be NaN.
+ * - If a channel has constant values, min/max/start/end will all be the same.
+ *
+ * @param image - The NgffImage to compute metadata for
+ * @param options - Optional configuration for quantiles, colors, and labels
+ *   - quantiles: Tuple of (low, high) quantile values. Must be between 0 and 1,
+ *                with low < high. Default is [0.02, 0.98] for 2% and 98% quantiles.
+ *   - colors: List of hex color strings (without #) for each channel.
+ *             Must be 6-digit hexadecimal strings (e.g., "FF0000" for red).
+ *             If not provided, uses white for single channel or Glasbey
+ *             progression for multi-channel.
+ *   - labels: List of label strings for each channel.
+ *             If not provided, uses empty strings.
+ * @returns Promise resolving to Omero metadata with computed window parameters
+ * @throws {Error} If quantiles are invalid, colors are invalid format,
+ *                 or not enough colors/labels provided.
+ *
+ * @example
+ * ```ts
+ * const omero = await computeOmeroFromNgffImage(image);
+ * multiscales.metadata.omero = omero;
+ * ```
+ */
+export async function computeOmeroFromNgffImage(image, options = {}) {
+    const quantiles = options.quantiles ?? [0.02, 0.98];
+    // Validate quantiles
+    validateQuantiles(quantiles);
+    const dims = image.dims;
+    const shape = image.data.shape;
+    // Check if there's a channel dimension
+    const hasChannelDim = dims.includes("c");
+    const cIndex = hasChannelDim ? dims.indexOf("c") : -1;
+    const nChannels = hasChannelDim ? shape[cIndex] : 1;
+    // Get colors
+    let channelColors;
+    if (options.colors !== undefined) {
+        if (options.colors.length < nChannels) {
+            throw new Error(`Not enough colors provided. Got ${options.colors.length}, need ${nChannels}.`);
+        }
+        // Validate each color
+        for (const color of options.colors.slice(0, nChannels)) {
+            validateColor(color);
+        }
+        channelColors = options.colors.slice(0, nChannels);
+    }
+    else {
+        channelColors = getDefaultColors(nChannels);
+    }
+    // Get labels
+    let channelLabels;
+    if (options.labels !== undefined) {
+        if (options.labels.length < nChannels) {
+            throw new Error(`Not enough labels provided. Got ${options.labels.length}, need ${nChannels}.`);
+        }
+        channelLabels = options.labels.slice(0, nChannels);
+    }
+    else {
+        channelLabels = Array(nChannels).fill("");
+    }
+    // Read all data from the zarr array
+    const result = await zarr.get(image.data);
+    const fullData = result.data;
+    // Compute statistics for each channel
+    const channels = [];
+    for (let chIdx = 0; chIdx < nChannels; chIdx++) {
+        let channelData;
+        if (hasChannelDim) {
+            // Extract this channel's data
+            channelData = extractChannel(fullData, shape, chIdx, cIndex);
+        }
+        else {
+            channelData = fullData;
+        }
+        // Compute statistics
+        const stats = computeChannelStatistics(channelData, quantiles);
+        // Create OMERO window
+        const window = {
+            min: stats.min,
+            max: stats.max,
+            start: stats.qLow,
+            end: stats.qHigh,
+        };
+        // Create channel metadata
+        const channel = {
+            color: channelColors[chIdx],
+            window,
+            label: channelLabels[chIdx],
+        };
+        channels.push(channel);
+    }
+    return { channels };
+}
+/**
+ * Compute OMERO metadata from a Multiscales object.
+ *
+ * This is a convenience function that computes OMERO metadata from the
+ * highest or lowest resolution image in a multiscales pyramid.
+ *
+ * @param multiscales - The Multiscales object to compute metadata for
+ * @param options - Optional configuration for quantiles, colors, labels, and resolution
+ * @returns Promise resolving to Omero metadata with computed window parameters
+ */
+export async function computeOmeroFromMultiscales(multiscales, options = {}) {
+    if (!multiscales.images || multiscales.images.length === 0) {
+        throw new Error("Multiscales has no images");
+    }
+    const useLowestResolution = options.useLowestResolution ?? true;
+    // Select which image to use based on resolution preference
+    const image = useLowestResolution
+        ? multiscales.images[multiscales.images.length - 1] // Last image (lowest resolution)
+        : multiscales.images[0]; // First image (highest resolution)
+    const computeOptions = {};
+    if (options.quantiles !== undefined) {
+        computeOptions.quantiles = options.quantiles;
+    }
+    if (options.colors !== undefined) {
+        computeOptions.colors = options.colors;
+    }
+    if (options.labels !== undefined) {
+        computeOptions.labels = options.labels;
+    }
+    return await computeOmeroFromNgffImage(image, computeOptions);
+}
+//# sourceMappingURL=compute_omero.js.map

package/esm/utils/compute_omero.js.map

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

@@ -1,10 +1,11 @@
 import { NgffImage } from "../types/ngff_image.js";
 import { Multiscales } from "../types/multiscales.js";
-import type { Axis, Dataset, Metadata, Scale, Translation } from "../types/zarr_metadata.js";
+import type { Axis, AxisOrientation, 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";
+import type { AnatomicalOrientation } from "../types/rfc4.js";
 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 createAxis(name: SupportedDims, type: AxesType, unit?: Units, orientation?: AxisOrientation | AnatomicalOrientation): Axis;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;
 export declare function createDataset(path: string, scale: number[], translation: number[]): Dataset;

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

@@ -1 +1 @@
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package/esm/utils/factory.js

@@ -27,12 +27,16 @@ export async function createNgffImage(_data, shape, dtype, dims, scale, translat
         computedCallbacks: undefined,
     });
 }
-export function createAxis(name, type, unit) {
-    return {
+export function createAxis(name, type, unit, orientation) {
+    const axis = {
         name,
         type,
         unit: unit || undefined,
     };
+    if (orientation) {
+        axis.orientation = orientation;
+    }
+    return axis;
 }
 export function createScale(scale) {
     return {

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package/esm/utils/from_zarr_attrs.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Functions for parsing Metadata from zarr store attributes.
+ */
+import * as zarr from "zarrita";
+import type { FromZarrAttrsResult } from "../types/zarr_metadata.js";
+import type { MemoryStore } from "../io/from_ngff_zarr.js";
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.4 root attributes.
+ *
+ * This mirrors the Python `Metadata._from_zarr_attrs` class method.
+ */
+export declare function fromZarrAttrsV04(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.5 root attributes.
+ *
+ * The v0.5 format typically wraps multiscales under the "ome" key,
+ * but for compatibility we also handle the case where multiscales
+ * is at the root level (as written by toNgffZarr).
+ */
+export declare function fromZarrAttrsV05(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
+//# sourceMappingURL=from_zarr_attrs.d.ts.map

package/esm/utils/from_zarr_attrs.d.ts.map

@@ -0,0 +1 @@
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