@fideus-labs/ngff-zarr 0.2.4 → 0.2.5

package/README.md

@@ -1,81 +1,273 @@
 <!-- SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC -->
 <!-- SPDX-License-Identifier: MIT -->
-# ngff-zarr
-
-[![PyPI - Version](https://img.shields.io/pypi/v/ngff-zarr.svg)](https://pypi.org/project/ngff-zarr)
-[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ngff-zarr.svg)](https://pypi.org/project/ngff-zarr)
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-[![DOI](https://zenodo.org/badge/541840158.svg)](https://zenodo.org/badge/latestdoi/541840158)
-[![Documentation Status](https://readthedocs.org/projects/ngff-zarr/badge/?version=latest)](https://ngff-zarr.readthedocs.io/en/latest/?badge=latest)
-
----
-
-A multi-language implementation of the
-[Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr](https://ngff.openmicroscopy.org)
-specification.
-
-## Repository Structure
-
-This repository contains multiple packages implementing NGFF-Zarr support:
-
-- **[`py/`](./py/)** - Python package (ngff-zarr) - A lean and kind NGFF-Zarr
-  implementation
-- **[`mcp/`](./mcp/)** - Model Context Protocol (MCP) server (ngff-zarr-mcp) for
-  AI integration
-- **TypeScript package** - Coming soon
-
-## Python Package (`py/`)
-
-The main Python package provides:
-
-✨ **Features**
-
-- Minimal dependencies
-- Work with arbitrary Zarr store types
-- Lazy, parallel, and web ready -- no local filesystem required
-- Process extremely large datasets
-- Conversion of most bioimaging file formats
-- Multiple downscaling methods
-- Supports Python>=3.9
-- Reads OME-Zarr v0.1 to v0.5 into simple Python data classes with Dask arrays
-- Optional OME-Zarr data model validation during reading
-- Writes OME-Zarr v0.4 to v0.5
-- [Sharded Zarr] stores
-- Optional writing via zarr-python 2, zarr-python 3, [tensorstore] or zarrita (TypeScript)
-- [Anatomical orientation metadata](./docs/rfc4.md) (RFC-4)
-- **OME-Zarr Zip (.ozx) file support** for single-file OME-Zarr datasets (RFC-9)
-- **High Content Screening (HCS) support** for plate and well data
-- **Model Context Protocol (MCP) server** for AI agent integration
-
-📖 **Documentation**
-
-More information about command line usage, the Python API, library features, and
-how to contribute can be found in
-[our documentation](https://ngff-zarr.readthedocs.io/).
-
-## MCP Server (`mcp/`)
-
-The Model Context Protocol server enables AI assistants like Claude to interact
-with NGFF-Zarr files. See the [MCP documentation](./mcp/README.md) for setup and
-usage instructions.
-
-## See also
-
-- [ome-zarr-py](https://github.com/ome/ome-zarr-py)
-- [multiscale-spatial-image](https://github.com/spatial-image/multiscale-spatial-image)
-- [itk-ioomezarrngff](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF)
-- [iohub](https://czbiohub-sf.github.io/iohub/)
-- [pydantic-ome-ngff](https://janeliascicomp.github.io/pydantic-ome-ngff/)
-- [aicsimageio](https://allencellmodeling.github.io/aicsimageio/)
-- [bfio](https://bfio.readthedocs.io/)
-- [zod-ome-ngff](https://github.com/hms-dbmi/zod-ome-ngff)
 
-## License
+# ngff-zarr TypeScript
+
+A TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files,
+compatible with Deno, Node.js, and the browser.
+
+## Features
+
+- 🦕 **Deno-first**: Built for Deno with first-class TypeScript support
+- 📦 **npm compatible**: Automatically builds npm packages using @deno/dnt
+- 🔍 **Type-safe**: Full TypeScript support with Zod schema validation
+- 🗂️ **OME-Zarr support**: Read and write OME-Zarr files using zarrita
+- 🧪 **Well-tested**: Comprehensive test suite using @std/assert
+- 🏗️ **Mirrors Python API**: TypeScript classes and types mirror the Python
+  dataclasses
+
+## Installation
+
+### Deno
+
+```typescript
+import * as ngffZarr from "@fideus-labs/ngff-zarr";
+```
+
+### Node.js/npm
+
+```bash
+npm install @fideus-labs/ngff-zarr
+```
+
+```typescript
+import * as ngffZarr from "@fideus-labs/ngff-zarr";
+```
+
+## Quick Start
+
+### Reading OME-Zarr files
+
+```typescript
+import { OMEZarrReader } from "@fideus-labs/ngff-zarr";
+
+const reader = new OMEZarrReader({ validate: true });
+const multiscales = await reader.fromNgffZarr("path/to/image.ome.zarr");
+
+console.log(`Loaded ${multiscales.images.length} scale levels`);
+console.log(`Image shape: ${multiscales.images[0].data.shape}`);
+```
+
+### Writing OME-Zarr files
+
+```typescript
+import {
+  createMetadata,
+  createMultiscales,
+  createNgffImage,
+  OMEZarrWriter,
+} from "@fideus-labs/ngff-zarr";
+
+// Create a simple 2D image
+const image = createNgffImage(
+  new ArrayBuffer(256 * 256),
+  [256, 256],
+  "uint8",
+  ["y", "x"],
+  { y: 1.0, x: 1.0 },
+  { y: 0.0, x: 0.0 },
+);
+
+// Create metadata
+const axes = [
+  { name: "y", type: "space" },
+  { name: "x", type: "space" },
+];
+const datasets = [{
+  path: "0",
+  coordinateTransformations: [
+    { type: "scale", scale: [1.0, 1.0] },
+    { type: "translation", translation: [0.0, 0.0] },
+  ],
+}];
+const metadata = createMetadata(axes, datasets);
+
+// Create multiscales
+const multiscales = createMultiscales([image], metadata);
+
+// Write to OME-Zarr
+const writer = new OMEZarrWriter();
+await writer.toNgffZarr("output.ome.zarr", multiscales);
+```
+
+### Schema Validation
+
+```typescript
+import { MetadataSchema, validateMetadata } from "@fideus-labs/ngff-zarr";
+
+const metadata = {
+  axes: [
+    { name: "y", type: "space" },
+    { name: "x", type: "space" },
+  ],
+  datasets: [{
+    path: "0",
+    coordinateTransformations: [
+      { type: "scale", scale: [1.0, 1.0] },
+      { type: "translation", translation: [0.0, 0.0] },
+    ],
+  }],
+  name: "test_image",
+  version: "0.4",
+};
+
+// Validate using Zod schema
+const validatedMetadata = MetadataSchema.parse(metadata);
+
+// Or use utility function
+const validatedMetadata2 = validateMetadata(metadata);
+```
+
+## API Reference
+
+### Core Types
+
+- `NgffImage`: Represents an image with associated metadata
+- `Multiscales`: Container for multiple scale levels of an image
+- `DaskArray`: Metadata representation of dask arrays
+- `Metadata`: OME-Zarr metadata structure
+
+### I/O Classes
+
+- `OMEZarrReader`: Read OME-Zarr files using zarrita
+- `OMEZarrWriter`: Write OME-Zarr files using zarrita
+
+### Validation
+
+- Zod schemas for all data structures
+- Utility functions for validation
+- Type-safe parsing and validation
+
+### Factory Functions
 
-`ngff-zarr` is distributed under the terms of the
-[MIT](https://spdx.org/licenses/MIT.html) license.
+- `createNgffImage()`: Create NgffImage instances
+- `createMetadata()`: Create metadata structures
+- `createMultiscales()`: Create multiscale containers
+
+## Development
+
+### Prerequisites
+
+- [Deno](https://deno.land/) >= 1.40.0
+- [Pixi](https://pixi.sh/) (optional, for environment management)
+
+### Setup
+
+```bash
+cd ts/
+pixi install  # or ensure Deno is installed
+```
+
+### Commands
+
+```bash
+# Run tests
+pixi run test
+# or
+deno test --allow-all
+
+# Format code
+pixi run fmt
+# or
+deno fmt
+
+# Lint code
+pixi run lint
+# or
+deno lint
+
+# Type check
+pixi run check
+# or
+deno check src/mod.ts
+
+# Build npm package
+pixi run build-npm
+# or
+deno task build:npm
+
+# Browser testing with Playwright
+pixi run test-browser
+# or
+deno task test:browser
+
+# Browser testing with UI
+deno task test:browser:ui
+
+# Run all tests (including browser tests)
+deno task test:all
+```
+
+### Browser Testing
+
+This project includes comprehensive browser testing using Playwright. The
+browser tests verify that the npm-transpiled package works correctly in real
+browser environments.
+
+**Features:**
+
+- Multi-browser testing (Chrome, Firefox, Safari, Mobile)
+- NPM package validation in browser context
+- Import resolution testing for dependencies
+- Schema validation in browser environment
+
+**Quick Start:**
+
+```bash
+# Build npm package and run browser tests
+deno task test:browser:npm
+
+# Run browser tests with interactive UI
+deno task test:browser:ui
+
+# Debug browser tests
+deno task test:browser:debug
+```
+
+**Test Files:**
+
+- `/test/browser-npm/` - Browser test files and configuration
+- `/test/browser/server.ts` - Test server for serving assets
+- `/scripts/run_playwright.mjs` - Node.js wrapper for Playwright execution
+
+See [test/browser/README.md](test/browser/README.md) for detailed browser
+testing documentation.
+
+### Project Structure
+
+```
+ts/
+├── src/
+│   ├── types/          # TypeScript type definitions
+│   ├── schemas/        # Zod validation schemas
+│   ├── io/            # Zarr I/O operations
+│   ├── utils/         # Utility functions
+│   └── mod.ts         # Main module exports
+├── test/              # Test files
+├── scripts/           # Build scripts
+├── deno.json          # Deno configuration
+├── pixi.toml          # Pixi environment
+└── README.md
+```
+
+## Relationship to Python Package
+
+This TypeScript package mirrors the Python ngff-zarr package:
+
+- **Types**: TypeScript interfaces/classes correspond to Python dataclasses
+- **API**: Similar function names and patterns
+- **Validation**: Zod schemas provide runtime validation like Python
+- **I/O**: zarrita provides Zarr operations like zarr-python
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests
+5. Run the test suite: `deno test --allow-all`
+6. Submit a pull request
+
+## License
 
-[Sharded Zarr]: https://zarr.dev/zeps/accepted/ZEP0002.html
-[tensorstore]: https://google.github.io/tensorstore/
+MIT License - see LICENSE file for details.

package/esm/browser-mod.js

@@ -23,3 +23,4 @@ export { createAxis, createDataset, createMetadata, createMultiscales, createNgf
 export { getMethodMetadata } from "./utils/method_metadata.js";
 // Browser-compatible processing modules
 export * from "./process/to_multiscales-browser.js";
+//# sourceMappingURL=browser-mod.js.map

package/esm/browser-mod.js.map

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package/esm/io/from_ngff_zarr.d.ts.map

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package/esm/io/from_ngff_zarr.js

@@ -1,6 +1,5 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
-import * as dntShim from "../_dnt.shims.js";
 import * as zarr from "zarrita";
 import { Multiscales } from "../types/multiscales.js";
 import { NgffImage } from "../types/ngff_image.js";
@@ -22,7 +21,7 @@ store, options = {}) {
         }
         else {
             // For local paths, check if we're in a browser environment
-            if (typeof dntShim.dntGlobalThis !== "undefined") {
+            if (typeof window !== "undefined") {
                 throw new Error("Local file paths are not supported in browser environments. Use HTTP/HTTPS URLs instead.");
             }
             // Use dynamic import for FileSystemStore, ZipFileStore in Node.js/Deno environments
@@ -205,3 +204,4 @@ export async function readArrayData(storePath, arrayPath, selection) {
         throw new Error(`Failed to read array data: ${error instanceof Error ? error.message : String(error)}`);
     }
 }
+//# sourceMappingURL=from_ngff_zarr.js.map

package/esm/io/from_ngff_zarr.js.map

@@ -0,0 +1 @@
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package/esm/io/hcs.js

@@ -49,3 +49,4 @@ export function toHcsZarr(plate, store, _options = {}) {
         console.log(`Acquisitions: ${plate.acquisitions.length}`);
     }
 }
+//# sourceMappingURL=hcs.js.map

package/esm/io/hcs.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"hcs.js","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,IAAI,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAa5D;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,KAAsB,EACtB,UAA8B,EAAE;IAEhC,MAAM,EAAE,QAAQ,GAAG,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAEpE,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;IACrD,CAAC;IAED,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,wCAAwC;IACxC,iFAAiF;IACjF,MAAM,aAAa,GAAkB;QACnC,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACvC,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACpC,KAAK,EAAE;YACL,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;SAC7C;QACD,OAAO,EAAE,KAAK;QACd,YAAY,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC;QACnD,WAAW,EAAE,CAAC;QACd,IAAI,EAAE,YAAY;KACnB,CAAC;IAEF,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK;QACL,QAAQ,EAAE,aAAa;QACvB,aAAa;QACb,cAAc;KACf,CAAC,CAAC;AACL,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,SAAS,CACvB,KAAe,EACf,KAAsB,EACtB,WAA6B,EAAE;IAE/B,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,8BAA8B;IAC9B,OAAO,CAAC,GAAG,CAAC,2CAA2C,KAAK,EAAE,CAAC,CAAC;IAChE,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;IACpC,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,OAAO,CAAC,GAAG,CAAC,SAAS,KAAK,CAAC,IAAI,CAAC,MAAM,cAAc,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5E,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,iBAAiB,KAAK,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5D,CAAC;AACH,CAAC"}

package/esm/io/itk_image_to_ngff_image.js

@@ -125,3 +125,4 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
         computedCallbacks: undefined,
     });
 }
+//# sourceMappingURL=itk_image_to_ngff_image.js.map

package/esm/io/itk_image_to_ngff_image.js.map

@@ -0,0 +1 @@
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package/esm/io/ngff_image_to_itk_image.js

@@ -216,3 +216,4 @@ export async function ngffImageToItkImage(ngffImage, options = {}) {
     };
     return itkImage;
 }
+//# sourceMappingURL=ngff_image_to_itk_image.js.map

package/esm/io/ngff_image_to_itk_image.js.map

@@ -0,0 +1 @@
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package/esm/io/to_ngff_image.js

@@ -134,3 +134,4 @@ function calculateStride(shape) {
     }
     return stride;
 }
+//# sourceMappingURL=to_ngff_image.js.map

package/esm/io/to_ngff_image.js.map

@@ -0,0 +1 @@
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package/esm/io/to_ngff_zarr.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAGvD,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7D;AAED,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CA0Ff"}

package/esm/io/to_ngff_zarr.js

@@ -1,6 +1,5 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
-import * as dntShim from "../_dnt.shims.js";
 import * as zarr from "zarrita";
 import { createQueue } from "../utils/create_queue.js";
 export async function toNgffZarr(store, multiscales, options = {}) {
@@ -20,7 +19,7 @@ export async function toNgffZarr(store, multiscales, options = {}) {
         }
         else {
             // For local paths, check if we're in a browser environment
-            if (typeof dntShim.dntGlobalThis !== "undefined") {
+            if (typeof window !== "undefined") {
                 throw new Error("Local file paths are not supported in browser environments. Use a MemoryStore instead.");
             }
             // Use dynamic import for FileSystemStore in Node.js/Deno environments
@@ -318,3 +317,4 @@ function calculateChunkStride(chunkShape) {
     }
     return stride;
 }
+//# sourceMappingURL=to_ngff_zarr.js.map

package/esm/io/to_ngff_zarr.js.map

@@ -0,0 +1 @@
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package/esm/methods/itkwasm-browser.js

@@ -460,3 +460,4 @@ export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing) {
     }
     return multiscales;
 }
+//# sourceMappingURL=itkwasm-browser.js.map

package/esm/methods/itkwasm-browser.js.map

@@ -0,0 +1 @@
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package/esm/methods/itkwasm-node.js

@@ -465,3 +465,4 @@ export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing) {
     }
     return multiscales;
 }
+//# sourceMappingURL=itkwasm-node.js.map

package/esm/methods/itkwasm-node.js.map

@@ -0,0 +1 @@
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