test(ts): add test_multiscales_metadata_test.ts

Author: thewtex

ts/src/io/to_multiscales.ts

@@ -0,0 +1,208 @@
+import * as zarr from "zarrita";
+import { NgffImage } from "../types/ngff_image.ts";
+import { Multiscales } from "../types/multiscales.ts";
+import { Methods } from "../types/methods.ts";
+import type { MemoryStore } from "../io/from_ngff_zarr.ts";
+import {
+  createAxis,
+  createDataset,
+  createMetadata,
+  createMultiscales,
+} from "../utils/factory.ts";
+import { getMethodMetadata } from "../utils/method_metadata.ts";
+
+export interface ToNgffImageOptions {
+  dims?: string[];
+  scale?: Record<string, number>;
+  translation?: Record<string, number>;
+  name?: string;
+}
+
+/**
+ * Convert array data to NgffImage
+ *
+ * @param data - Input data as typed array or regular array
+ * @param options - Configuration options for NgffImage creation
+ * @returns NgffImage instance
+ */
+export async function toNgffImage(
+  data: ArrayLike<number> | number[][] | number[][][],
+  options: ToNgffImageOptions = {},
+): Promise<NgffImage> {
+  const {
+    dims = ["y", "x"],
+    scale = {},
+    translation = {},
+    name = "image",
+  } = options;
+
+  // Determine data shape and create typed array
+  let typedData: Float32Array;
+  let shape: number[];
+
+  if (Array.isArray(data)) {
+    // Handle multi-dimensional arrays
+    if (Array.isArray(data[0])) {
+      if (Array.isArray((data[0] as unknown[])[0])) {
+        // 3D array
+        const d3 = data as number[][][];
+        shape = [d3.length, d3[0].length, d3[0][0].length];
+        typedData = new Float32Array(shape[0] * shape[1] * shape[2]);
+
+        let idx = 0;
+        for (let i = 0; i < shape[0]; i++) {
+          for (let j = 0; j < shape[1]; j++) {
+            for (let k = 0; k < shape[2]; k++) {
+              typedData[idx++] = d3[i][j][k];
+            }
+          }
+        }
+      } else {
+        // 2D array
+        const d2 = data as number[][];
+        shape = [d2.length, d2[0].length];
+        typedData = new Float32Array(shape[0] * shape[1]);
+
+        let idx = 0;
+        for (let i = 0; i < shape[0]; i++) {
+          for (let j = 0; j < shape[1]; j++) {
+            typedData[idx++] = d2[i][j];
+          }
+        }
+      }
+    } else {
+      // 1D array
+      const d1 = data as unknown as number[];
+      shape = [d1.length];
+      typedData = new Float32Array(d1);
+    }
+  } else {
+    // ArrayLike (already a typed array)
+    typedData = new Float32Array(data as ArrayLike<number>);
+    shape = [typedData.length];
+  }
+
+  // Adjust shape to match dims length
+  while (shape.length < dims.length) {
+    shape.unshift(1);
+  }
+
+  if (shape.length > dims.length) {
+    throw new Error(
+      `Data dimensionality (${shape.length}) exceeds dims length (${dims.length})`,
+    );
+  }
+
+  // Create in-memory zarr store and array
+  const store: MemoryStore = new Map();
+  const root = zarr.root(store);
+
+  // Calculate appropriate chunk size
+  const chunkShape = shape.map((dim) => Math.min(dim, 256));
+
+  const zarrArray = await zarr.create(root.resolve("data"), {
+    shape,
+    chunk_shape: chunkShape,
+    data_type: "float32",
+    fill_value: 0,
+  });
+
+  // Write data to zarr array
+  await zarr.set(zarrArray, [], {
+    data: typedData,
+    shape,
+    stride: calculateStride(shape),
+  });
+
+  // Create scale and translation records with defaults
+  const fullScale: Record<string, number> = {};
+  const fullTranslation: Record<string, number> = {};
+
+  for (const dim of dims) {
+    fullScale[dim] = scale[dim] ?? 1.0;
+    fullTranslation[dim] = translation[dim] ?? 0.0;
+  }
+
+  return new NgffImage({
+    data: zarrArray,
+    dims,
+    scale: fullScale,
+    translation: fullTranslation,
+    name,
+    axesUnits: undefined,
+    computedCallbacks: undefined,
+  });
+}
+
+export interface ToMultiscalesOptions {
+  scaleFactors?: (Record<string, number> | number)[];
+  method?: Methods;
+  chunks?: number | number[] | Record<string, number>;
+}
+
+/**
+ * Generate multiple resolution scales for an NgffImage (simplified version for testing)
+ *
+ * @param image - Input NgffImage
+ * @param options - Configuration options
+ * @returns Multiscales object
+ */
+export function toMultiscales(
+  image: NgffImage,
+  options: ToMultiscalesOptions = {},
+): Multiscales {
+  const {
+    scaleFactors = [2, 4],
+    method = Methods.ITKWASM_GAUSSIAN,
+    chunks: _chunks,
+  } = options;
+
+  // For now, create only the base image (no actual downsampling)
+  // This is a simplified implementation for testing metadata functionality
+  const images = [image];
+
+  // Create axes from image dimensions
+  const axes = image.dims.map((dim) => {
+    if (dim === "x" || dim === "y" || dim === "z") {
+      return createAxis(
+        dim as "x" | "y" | "z",
+        "space",
+        image.axesUnits?.[dim],
+      );
+    } else if (dim === "c") {
+      return createAxis(dim as "c", "channel");
+    } else if (dim === "t") {
+      return createAxis(dim as "t", "time");
+    } else {
+      throw new Error(`Unsupported dimension: ${dim}`);
+    }
+  });
+
+  // Create datasets
+  const datasets = [
+    createDataset(
+      "0",
+      image.dims.map((dim) => image.scale[dim]),
+      image.dims.map((dim) => image.translation[dim]),
+    ),
+  ];
+
+  // Create metadata with method information
+  const methodMetadata = getMethodMetadata(method);
+  const metadata = createMetadata(axes, datasets, image.name);
+  metadata.type = method;
+  if (methodMetadata) {
+    metadata.metadata = methodMetadata;
+  }
+
+  return createMultiscales(images, metadata, scaleFactors, method);
+}
+
+function calculateStride(shape: number[]): number[] {
+  const stride = new Array(shape.length);
+  stride[shape.length - 1] = 1;
+  for (let i = shape.length - 2; i >= 0; i--) {
+    stride[i] = stride[i + 1] * shape[i + 1];
+  }
+  return stride;
+}

ts/src/io/to_ngff_zarr.ts

@@ -68,6 +68,12 @@ export async function toNgffZarr(
               coordinateTransformations:
                 multiscales.metadata.coordinateTransformations,
             }),
+            ...(multiscales.metadata.type && {
+              type: multiscales.metadata.type,
+            }),
+            ...(multiscales.metadata.metadata && {
+              metadata: multiscales.metadata.metadata,
+            }),
           },
         ],
         ...(multiscales.metadata.omero && {

ts/src/mod.ts

@@ -25,9 +25,11 @@ export {
   createMultiscales,
   createNgffImage,
 } from "./utils/factory.ts";
+export { getMethodMetadata } from "./utils/method_metadata.ts";
 
 export * from "./io/from_ngff_zarr.ts";
 export * from "./io/to_ngff_zarr.ts";
+export * from "./io/to_multiscales.ts";
 export type { MemoryStore } from "./io/from_ngff_zarr.ts";
 export * from "./io/itk_image_to_ngff_image.ts";
 export * from "./io/ngff_image_to_itk_image.ts";

ts/src/schemas/zarr_metadata.ts

@@ -81,18 +81,28 @@ export const OmeroSchema: z.ZodObject<{
   channels: z.array(OmeroChannelSchema),
 });
 
+export const MethodMetadataSchema = z.object({
+  description: z.string(),
+  method: z.string(),
+  version: z.string(),
+});
+
 export const MetadataSchema: z.ZodObject<{
   axes: z.ZodArray<typeof AxisSchema>;
   datasets: z.ZodArray<typeof DatasetSchema>;
   coordinateTransformations: z.ZodOptional<z.ZodArray<typeof TransformSchema>>;
   omero: z.ZodOptional<typeof OmeroSchema>;
   name: z.ZodDefault<z.ZodString>;
   version: z.ZodDefault<z.ZodString>;
+  type: z.ZodOptional<z.ZodString>;
+  metadata: z.ZodOptional<typeof MethodMetadataSchema>;
 }> = z.object({
   axes: z.array(AxisSchema),
   datasets: z.array(DatasetSchema),
   coordinateTransformations: z.array(TransformSchema).optional(),
   omero: OmeroSchema.optional(),
   name: z.string().default("image"),
   version: z.string().default("0.4"),
+  type: z.string().optional(),
+  metadata: MethodMetadataSchema.optional(),
 });

ts/src/types/zarr_metadata.ts

@@ -46,13 +46,21 @@ export interface Omero {
   version?: string;
 }
 
+export interface MethodMetadata {
+  description: string;
+  method: string;
+  version: string;
+}
+
 export interface Metadata {
   axes: Axis[];
   datasets: Dataset[];
   coordinateTransformations: Transform[] | undefined;
   omero: Omero | undefined;
   name: string;
   version: string;
+  type?: string;
+  metadata?: MethodMetadata;
 }
 
 export function validateColor(color: string): void {

ts/src/utils/method_metadata.ts

@@ -0,0 +1,52 @@
+import type { Methods } from "../types/methods.ts";
+import type { MethodMetadata } from "../types/zarr_metadata.ts";
+
+interface MethodInfo {
+  description: string;
+  package: string;
+  method: string;
+}
+
+const METHOD_INFO: Record<string, MethodInfo> = {
+  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
+ */
+export function getMethodMetadata(method: Methods): MethodMetadata | undefined {
+  const methodInfo = METHOD_INFO[method];
+  if (!methodInfo) {
+    return undefined;
+  }
+
+  // For TypeScript/browser environment, we can't easily get package versions
+  // so we'll use a placeholder or try to infer from known versions
+  const version = "unknown";
+
+  return {
+    description: methodInfo.description,
+    method: methodInfo.method,
+    version,
+  };
+}