diff --git a/.changeset/legal-moles-design.md b/.changeset/legal-moles-design.md new file mode 100644 index 00000000..f2c4e2de --- /dev/null +++ b/.changeset/legal-moles-design.md @@ -0,0 +1,10 @@ +--- +"@spatialdata/avivatorish": patch +"zarrextra": patch +"@spatialdata/core": patch +"@spatialdata/vis": patch +--- + +Add support for alternative codecs in zarrextra, with tooling to encode images as JPEG2000 and HTJ2K. + +Zarrita stores can be configured to decode in workers. diff --git a/.cursor/settings.json b/.cursor/settings.json index 7ff7a3d4..55a61b03 100644 --- a/.cursor/settings.json +++ b/.cursor/settings.json @@ -9,7 +9,8 @@ "editor.formatOnSave": true }, "python.analysis.extraPaths": [ - "${workspaceFolder}/python" + "${workspaceFolder}/python", + "${workspaceFolder}/python/spatialdata-codec-writer/scripts" ] } diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 60b3ef30..35531b09 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -35,6 +35,9 @@ jobs: - name: Install dependencies run: pnpm install --frozen-lockfile + - name: Vendor OpenJPH for spatialdata-codec-writer + run: node scripts/vendor-openjph-for-python.mjs + - name: Build packages run: pnpm build @@ -51,6 +54,9 @@ jobs: - name: Generate test fixtures (Python spatialdata 0.5.0, 0.6.1, and 0.7.2) run: pnpm test:fixtures:generate + - name: Run spatialdata-codec-writer tests + run: uv run --directory python/spatialdata-codec-writer pytest + - name: Run unit tests run: pnpm test:unit diff --git a/.gitignore b/.gitignore index 1b21274a..611bca7d 100644 --- a/.gitignore +++ b/.gitignore @@ -19,6 +19,13 @@ python/v0.5.0/.venv/ python/v0.6.1/.venv/ python/v0.7.2/.venv/ +# Vendored from @cornerstonejs/codec-openjph (see scripts/vendor-openjph-for-python.mjs) +python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/openjph/ + +**/__pycache__/ +*.egg-info/ +*.egg + # Environment .env .env.local diff --git a/.vscode/settings.json b/.vscode/settings.json index f153c808..e031a03d 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -9,7 +9,8 @@ "editor.formatOnSave": true }, "python.analysis.extraPaths": [ - "${workspaceFolder}/python" + "${workspaceFolder}/python", + "${workspaceFolder}/python/spatialdata-codec-writer/scripts" ], "typescript.tsdk": "node_modules/typescript/lib" } diff --git a/AGENTS.md b/AGENTS.md index 78e8c3b8..d0c9eee9 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -26,5 +26,11 @@ joining work on this repository. - Treat layers as independent views of spatial elements: it must be valid for multiple layer configs to represent the same underlying element with different visual properties, filters, or table-driven encodings. +- Avoid type assertions (`as ...`) in TypeScript when a library overload, + local type guard, schema parser, discriminated union, or narrower API + contract can express the same fact. If an assertion is unavoidable at an + external boundary (for example an untyped WASM module or a TypeScript + correlation limitation), keep it local and add a short comment explaining why + the compiler cannot prove it. - Worktrees share `.git` but not working state. Documents intended to outlive the current branch must land on `main`. diff --git a/docs/docs/vis/codec-fixtures.mdx b/docs/docs/vis/codec-fixtures.mdx new file mode 100644 index 00000000..dcb34fa3 --- /dev/null +++ b/docs/docs/vis/codec-fixtures.mdx @@ -0,0 +1,191 @@ +--- +sidebar_position: 6 +--- + +# Codec fixture guide + +SpatialData codec fixtures live under `test-fixtures/codecs/` and are generated +separately from the versioned `blobs()` fixtures. The reference fixtures are +small OME-Zarr/SpatialData images using: + +- `imagecodecs_jpeg2k` (registered JP2K codec id) +- `experimental.openjph_htj2k` (OpenJPH WASM HTJ2K codec id) + +Generated stores include: + +- `jpeg2k.zarr` — small multiscale Mandelbrot (`[1,1,1,64,64]`) +- `mandelbulb.zarr` — multi-dimensional Mandelbulb volume (`[2,1,8,128,128]`, HTJ2K, one plane per t/z chunk) +- `htj2k.zarr` / `htj2k-demo.zarr` — HTJ2K smoke and encode-demo stores (when the WASM encoder is available) + +Older fixtures may use `experimental.imagecodecs_htj2k`; the frontend decodes both. + +## Try it in the browser + +From the repo root: + +```bash +pnpm test:fixtures:generate:codecs +pnpm --filter @spatialdata/vis dev +``` + +Open [http://127.0.0.1:5173/codec](http://127.0.0.1:5173/codec). + +The route calls `enableWorkerChunkDecode()` from `zarrextra/workers`, which uses +[`@fideus-labs/fizarrita`](https://www.npmjs.com/package/@fideus-labs/fizarrita) +with a custom codec worker that registers JP2K and experimental HTJ2K support +inside the worker before decode. Use the codec selector on the page to switch between `/test-fixtures/codecs/jpeg2k.zarr`, +`/test-fixtures/codecs/mandelbulb.zarr`, and `/test-fixtures/codecs/htj2k-demo.zarr`. +When HTJ2K is selected, the demo loads a single `htj2k-demo.zarr` store containing +`mandelbrot_lossless`, `mandelbrot_balanced`, and `mandelbrot_small` image layers +(512×512 Mandelbrot, two pyramid levels). Use the `SpatialCanvas` layer controls to +toggle between presets. Manifests are at +`/test-fixtures/codecs/jpeg2k.manifest.json`, +`/test-fixtures/codecs/mandelbulb.manifest.json`, and +`/test-fixtures/codecs/htj2k-encode-demo.manifest.json`. + +The vis dev script starts the fixture server on port `38473` and proxies +`/test-fixtures` through Vite on `5173`. Override the fixture server port with +`SPATIALDATA_FIXTURE_PORT` if needed. + +## Python reference writer + +The **publishable** package (`spatialdata-codec-writer`) exposes recompression +only. Codec test fixtures are generated by repo-local scripts under +`python/spatialdata-codec-writer/scripts/`. + +Useful commands: + +```bash +pnpm test:fixtures:generate:codecs +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer inspect ../../test-fixtures/codecs/jpeg2k.manifest.json +``` + +### Fixture provenance + +Dev fixtures stamp root metadata with an experimental marker rather than a fake +`spatialdata` library version: + +```json +"spatialdata_attrs": { + "experimental_codec_writer": "0.1.0", + "note": "codec test fixture; not a spatialdata.write() artifact" +} +``` + +The frontend image schema treats `spatialdata_attrs` as optional on rasters and +does not use `version` for OME format detection. We intend to propose a +standardized provenance field to the spatialdata community; feedback welcome. + +The sidecar manifest records shape, dtype, chunk shape, codec id, package +versions, and representative decoded/encoded checksums. The fixture scripts +validate representative chunks after writing so JS tests can compare decoded +samples against Python. + +### Whole-object recompression + +For larger or real examples, use the `recompress` command. It copies the source +SpatialData store, rewrites configured image rasters with JP2K or experimental +HTJ2K, and writes labels with Blosc/zstd by default. + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress input.sdata.zarr output-jp2k.zarr --image-key morphology_focus --preset balanced --chunks auto --overwrite +``` + +Custom HTJ2K quality (instead of a preset name): + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress \ + input.sdata.zarr output-htj2k.zarr \ + --image-key morphology_focus \ + --codec experimental.openjph_htj2k \ + --quality 0.001 \ + --chunks auto \ + --sibling \ + --overwrite +``` + +`--quality` requires `--image-key` and `--codec experimental.openjph_htj2k`. +Lower values preserve more detail. With `--sibling`, the output image is named +like `morphology_focus:htj2k_q0.001`. + +For repeatable per-raster settings, use JSON: + +```json +{ + "default_image": { "codec": "imagecodecs_jpeg2k", "preset": "lossless", "chunks": "auto" }, + "images": { + "morphology_focus": { "preset": "balanced" }, + "morphology_focus_htj2k_tuned": { + "codec": "experimental.openjph_htj2k", + "quality": 0.001, + "chunks": "auto" + }, + "he_image": { "preset": "small" }, + "fast_preview": { + "codec": "experimental.openjph_htj2k", + "preset": "lossless", + "chunks": "auto" + } + }, + "default_labels": { "codec": "blosc", "clevel": 5 } +} +``` + +JP2K and HTJ2K share preset names (`lossless`, `balanced`, `small`). HTJ2K encode +uses OpenJPH WASM (`experimental.openjph_htj2k`) via +`HTJ2KEncoder.setQuality(reversible, quality)`. The quality argument is a float +quantization factor (lower = higher fidelity, larger output) — not JP2K-style +0–100. Presets map to `balanced: 0.0002`, `small: 0.001` (calibrated roughly on +Xenium morphology; see `python/spatialdata-codec-writer/docs/htj2k-wasm-encode-design.md`). +Override with CLI `--quality 0.001` or per-image JSON `"quality": 0.001` (implies +lossy unless `"reversible": true`). A future codec-demo UI may add interactive `q` +exploration on sample regions. + +`generate_codec_fixtures.py --experimental-htj2k` also writes +`htj2k-quality-sweep.manifest.json`, encoding the same Mandelbrot plane at several +qualities so you can confirm compression responds on detail-rich imagery, and +`htj2k-encode-demo.manifest.json` with three browser-viewable multiscale image +layers in one store (`htj2k-demo.zarr`: `mandelbrot_lossless`, `mandelbrot_balanced`, +`mandelbrot_small`) at 512×512 with 64×64 chunks. The main `htj2k.zarr` fixture +remains a small 64×64 Mandelbrot raster for fast CI smoke tests. +`mandelbulb.zarr` exercises multi `t`/`z` HTJ2K decode in JS (`images/mandelbulb`, shape +`[2, 1, 8, 128, 128]`, chunks `(1, 1, 1, 128, 128)`). + +Browser-targeted image codec output is limited to `uint8`, `int8`, `uint16`, and +`int16`. Labels are not image-codec-compressed in v1; they stay lossless through +Blosc/zstd because integer IDs and wider dtypes such as `uint32` are not +considered supported by the current JavaScript decoder paths. + +Useful Xenium morphology experiment: + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress /path/to/input.zarr /path/to/output.zarr --image-key morphology_focus --preset balanced --chunks auto --overwrite +``` + +When serving recompressed stores for browser experiments, disable HTTP caching +or use a fresh output path after each rewrite. `http-server` defaults to +cacheable responses, so overwriting a Zarr store in place can leave the browser +with stale array metadata that points at the old codec while the chunk bytes have +changed. + +```bash +bunx http-server --cors -c-1 /private/tmp +``` + +Repo scripts may set `UV_CACHE_DIR=.tmp/uv-cache` for sandbox or CI cache +isolation, but normal user-facing `uv run` commands do not need it. + +## JS codec flow + +`zarrextra` exposes: + +- `registerJpeg2kCodec()` for the registered `imagecodecs_jpeg2k` id (Node/CI). +- `enableWorkerChunkDecode()` from `zarrextra/workers` for browser apps (fizarrita + worker pool + custom codec worker with JP2K and experimental HTJ2K registration). +- `registerExperimentalHtj2kCodec()` for OpenJPH HTJ2K decode (`experimental.openjph_htj2k` + and legacy `experimental.imagecodecs_htj2k`) in Node/CI smoke tests. +- `loadOmeZarrMultiscalesFromStore()` for loading multiscales from a + `zarr.Readable` store without going back through Viv's URL loader. + +`@spatialdata/vis` now prefers raster element stores (`images/` and +`labels/`) and keeps Viv URL loading as a compatibility fallback. diff --git a/docs/docs/vis/headless-viewer.mdx b/docs/docs/vis/headless-viewer.mdx index dbc86f62..9c171ed3 100644 --- a/docs/docs/vis/headless-viewer.mdx +++ b/docs/docs/vis/headless-viewer.mdx @@ -212,6 +212,9 @@ Open **http://127.0.0.1:5173/headless** for the headless demo route. It loads the local **`blobs.zarr`** fixture (`v0.7.2`) via `SpatialCanvasViewer` with externally controlled layer state — no `SpatialCanvas` sidebars. +Open **http://127.0.0.1:5173/codec** for the JP2K codec fixture route. Generate +it first with `pnpm test:fixtures:generate:codecs`. + The dev script starts the fixture server on port **38473** (override with `SPATIALDATA_FIXTURE_PORT`) and proxies `/test-fixtures` through Vite on **5173**. The default Sketch UI remains at **http://127.0.0.1:5173/**. diff --git a/package.json b/package.json index e8cf4f12..258ee60c 100644 --- a/package.json +++ b/package.json @@ -20,6 +20,9 @@ "test:fixtures:generate:0.5.0": "uv run python/scripts/generate_fixtures.py --version 0.5.0", "test:fixtures:generate:0.6.1": "uv run python/scripts/generate_fixtures.py --version 0.6.1", "test:fixtures:generate:0.7.2": "uv run python/scripts/generate_fixtures.py --version 0.7.2", + "test:fixtures:generate:codecs": "node scripts/vendor-openjph-for-python.mjs && UV_CACHE_DIR=.tmp/uv-cache uv run --directory python/spatialdata-codec-writer python scripts/generate_codec_fixtures.py --output-dir ../../test-fixtures/codecs --experimental-htj2k --overwrite", + "write-synthetic": "node scripts/vendor-openjph-for-python.mjs && uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer-write-synthetic", + "test:codec-writer": "node scripts/vendor-openjph-for-python.mjs && UV_CACHE_DIR=.tmp/uv-cache uv run --directory python/spatialdata-codec-writer pytest", "test:server": "node scripts/test-server.js", "test:proxy": "node scripts/cors-proxy.js", "validate:datasets:js": "node scripts/validate-datasets-js.js", diff --git a/packages/avivatorish/package.json b/packages/avivatorish/package.json index 735efc7e..bf1554e3 100644 --- a/packages/avivatorish/package.json +++ b/packages/avivatorish/package.json @@ -30,6 +30,7 @@ "@hms-dbmi/viv": "catalog:", "@math.gl/core": "catalog:", "geotiff": "2.1.4-beta.0", + "zarrextra": "workspace:*", "zustand": "^5.0.8" }, "devDependencies": { diff --git a/packages/avivatorish/src/omeZarrMultiscales.ts b/packages/avivatorish/src/omeZarrMultiscales.ts index faabcc60..0d847ad2 100644 --- a/packages/avivatorish/src/omeZarrMultiscales.ts +++ b/packages/avivatorish/src/omeZarrMultiscales.ts @@ -1,7 +1,28 @@ import { loadOmeZarr } from '@hms-dbmi/viv'; +import { loadOmeZarrMultiscalesFromStore } from 'zarrextra'; + +export type OmeZarrMultiscalesSource = + | string + | { + url?: string; + store?: unknown; + }; + +/** OME-Zarr multiscales pixel sources (no caching). */ +export async function loadOmeZarrMultiscalesData( + source: OmeZarrMultiscalesSource +): Promise { + if (typeof source !== 'string' && source.store) { + return await loadOmeZarrMultiscalesFromStore( + source.store as Parameters[0] + ); + } + + const url = typeof source === 'string' ? source : source.url; + if (!url) { + throw new Error('OME-Zarr loading requires either a Zarrita store or a URL.'); + } -/** OME-Zarr multiscales pixel sources for a URL (no caching). */ -export async function loadOmeZarrMultiscalesData(url: string): Promise { const loader = await loadOmeZarr(url, { type: 'multiscales' }); return loader.data; } diff --git a/packages/avivatorish/tsconfig.json b/packages/avivatorish/tsconfig.json index 26de4c46..169c0a9a 100644 --- a/packages/avivatorish/tsconfig.json +++ b/packages/avivatorish/tsconfig.json @@ -12,6 +12,11 @@ "esModuleInterop": true, "resolveJsonModule": true, "lib": ["ES2020", "DOM", "DOM.Iterable"], + "baseUrl": ".", + "paths": { + "zarrextra": ["../zarrextra/src/index.ts"], + "zarrextra/*": ["../zarrextra/src/*"] + }, "types": ["react", "react-dom"] }, "include": ["src", "vite.config.ts", "tests"], diff --git a/packages/avivatorish/vite.config.ts b/packages/avivatorish/vite.config.ts index 81f33e18..64e99744 100644 --- a/packages/avivatorish/vite.config.ts +++ b/packages/avivatorish/vite.config.ts @@ -7,7 +7,7 @@ const pkgRoot = fileURLToPath(new URL('.', import.meta.url)); const baseConfig = defineViteConfig({ pkgRoot, libName: 'SpatialDataAvivatorish', - external: ['@hms-dbmi/viv', '@math.gl/core', 'geotiff', /^zustand(?:\/.*)?$/], + external: ['@hms-dbmi/viv', '@math.gl/core', 'geotiff', 'zarrita', 'zarrextra', /^zustand(?:\/.*)?$/], }); export default mergeConfig(baseConfig, { diff --git a/packages/core/src/models/index.ts b/packages/core/src/models/index.ts index 99b5149c..253fef4e 100644 --- a/packages/core/src/models/index.ts +++ b/packages/core/src/models/index.ts @@ -1,34 +1,35 @@ -import type { - ElementName, - BadFileHandler, - SDataProps, - ZarrTree, - LazyZarrArray, - ZAttrsAny, - Result, - TableColumnData, -} from '../types'; -import { ATTRS_KEY } from '../types'; -import { Ok, Err } from '../types'; import * as ad from 'anndata.js'; +import { createPrefixedStore } from 'zarrextra'; import type * as zarr from 'zarrita'; -import SpatialDataShapesSource from './VShapesSource'; -import SpatialDataTableSource from './VTableSource'; import { - rasterAttrsSchema, - shapesAttrsSchema, - pointsAttrsSchema, + type CoordinateTransformation, + type PointsAttrs, type RasterAttrs, type ShapesAttrs, - type PointsAttrs, - type CoordinateTransformation, - tableAttrsSchema, type TableAttrs, + pointsAttrsSchema, + rasterAttrsSchema, + shapesAttrsSchema, + tableAttrsSchema, } from '../schemas'; -import { type BaseTransformation, Identity, parseTransforms } from '../transformations'; -import SpatialDataPointsSource from './VPointsSource'; import type { ShapesRenderData } from '../shapes'; import { isSpatialData, loadFeatureRowIndexByFeatureIndex } from '../tableAssociations'; +import { type BaseTransformation, Identity, parseTransforms } from '../transformations'; +import type { + BadFileHandler, + ElementName, + LazyZarrArray, + Result, + SDataProps, + TableColumnData, + ZAttrsAny, + ZarrTree, +} from '../types'; +import { ATTRS_KEY } from '../types'; +import { Err, Ok } from '../types'; +import SpatialDataPointsSource from './VPointsSource'; +import SpatialDataShapesSource from './VShapesSource'; +import SpatialDataTableSource from './VTableSource'; /** * Parameters for creating element instances. @@ -41,34 +42,6 @@ export type ElementParams = { onBadFiles?: BadFileHandler; }; -function toAbsolutePath(path: string): zarr.AbsolutePath { - const trimmed = path.replace(/^\/+|\/+$/g, ''); - return (trimmed ? `/${trimmed}` : '/') as zarr.AbsolutePath; -} - -function joinAbsolutePath(prefix: string, key: zarr.AbsolutePath): zarr.AbsolutePath { - const normalizedPrefix = toAbsolutePath(prefix); - if (normalizedPrefix === '/') { - return key; - } - if (key === '/') { - return normalizedPrefix; - } - return `${normalizedPrefix}${key}` as zarr.AbsolutePath; -} - -function createPrefixedStore(store: zarr.Readable, prefix: string): zarr.Readable { - return { - async get(key: zarr.AbsolutePath, opts?: zarr.GetOptions) { - return await store.get(joinAbsolutePath(prefix, key), opts); - }, - getRange: store.getRange - ? async (key: zarr.AbsolutePath, range: zarr.RangeQuery, opts?: zarr.GetOptions) => - await store.getRange?.(joinAbsolutePath(prefix, key), range, opts) - : undefined, - }; -} - // ============================================ // Abstract Base Classes // ============================================ @@ -388,6 +361,16 @@ abstract class RasterElement extends AbstractSpat return this.attrs.multiscales[0]?.datasets.map((d) => d.path) ?? []; } + /** + * Store view rooted at this raster element. + * + * Consumers that need codec-aware array loading should use this instead of + * reconstructing a URL and letting downstream libraries create their own store. + */ + getStore(): zarr.AsyncReadable { + return createPrefixedStore(this.sdata.rootStore.zarritaStore, this.path); + } + /** * For raster elements, transformations are in multiscales[0].coordinateTransformations. */ diff --git a/packages/vis/README.md b/packages/vis/README.md index 1e694278..036112c0 100644 --- a/packages/vis/README.md +++ b/packages/vis/README.md @@ -4,4 +4,15 @@ High-level React-components and deck.gl layers for visualising SpatialData. This It is hoped that it will be robust and of a high quality, but especially at the early stage of development, the goal is not to have a lean bundle size, guarantees of API stability between releases, etc. -It is used to provide working examples for displaying in the `docs` site, as well as a sample app primarily for prototyping while developing features. \ No newline at end of file +It is used to provide working examples for displaying in the `docs` site, as well as a sample app primarily for prototyping while developing features. + +## Local fixture demos + +```bash +pnpm test:fixtures:generate:0.7.2 +pnpm test:fixtures:generate:codecs +pnpm --filter @spatialdata/vis dev +``` + +- http://127.0.0.1:5173/headless loads the versioned `blobs.zarr` fixture. +- http://127.0.0.1:5173/codec loads local codec fixtures (JP2K smoke test, HTJ2K Mandelbulb volume, HTJ2K encode demo). diff --git a/packages/vis/demo/src/App.tsx b/packages/vis/demo/src/App.tsx index 1f376796..d794918f 100644 --- a/packages/vis/demo/src/App.tsx +++ b/packages/vis/demo/src/App.tsx @@ -1,14 +1,22 @@ +import { lazy, Suspense } from 'react'; import Sketch from '../../src/Sketch'; import HeadlessBlobsDemo from './HeadlessBlobsDemo'; -function getDemoRoute(): 'sketch' | 'headless' { +const CodecFixtureDemo = lazy(() => import('./CodecFixtureDemo')); + +type DemoRoute = 'sketch' | 'headless' | 'codec'; + +function getDemoRoute(): DemoRoute { if (typeof window === 'undefined') { return 'sketch'; } - return window.location.pathname.replace(/\/+$/, '').endsWith('/headless') ? 'headless' : 'sketch'; + const pathname = window.location.pathname.replace(/\/+$/, ''); + if (pathname.endsWith('/headless')) return 'headless'; + if (pathname.endsWith('/codec')) return 'codec'; + return 'sketch'; } -function DemoNav({ route }: { route: 'sketch' | 'headless' }) { +function DemoNav({ route }: { route: DemoRoute }) { const linkStyle = (active: boolean) => ({ color: active ? '#fff' : '#8af', fontWeight: active ? 600 : 400, @@ -24,6 +32,9 @@ function DemoNav({ route }: { route: 'sketch' | 'headless' }) { Headless blobs + + Codec fixture + ); } @@ -37,7 +48,17 @@ function App() {

@spatialdata/vis Demo

-
{route === 'headless' ? : }
+
+ {route === 'headless' ? ( + + ) : route === 'codec' ? ( + Loading codec demo...}> + + + ) : ( + + )} +
); } diff --git a/packages/vis/demo/src/CodecFixtureDemo.tsx b/packages/vis/demo/src/CodecFixtureDemo.tsx new file mode 100644 index 00000000..2812fabd --- /dev/null +++ b/packages/vis/demo/src/CodecFixtureDemo.tsx @@ -0,0 +1,457 @@ +import { SpatialDataProvider, useSpatialData } from '@spatialdata/react'; +import { useEffect, useMemo, useState } from 'react'; +import { type LayerConfig, SpatialCanvas, SpatialCanvasViewer, type ViewState } from '../../src/index'; +import { buildHeadlessLayersForCoordinateSystem } from './buildHeadlessLayers'; +import { + getLocalHtj2kEncodeDemoFixtureUrl, + getLocalHtj2kEncodeDemoManifestUrl, + getLocalJpeg2kCodecFixtureUrl, + getLocalJpeg2kCodecManifestUrl, + getLocalMandelbulbCodecFixtureUrl, + getLocalMandelbulbCodecManifestUrl, +} from './fixtureUrls'; + +type CodecFixtureKind = 'jpeg2k' | 'mandelbulb' | 'htj2k'; + +type Htj2kEncodeDemoVariant = { + label: string; + suffix: string; + image_key: string; + image_path: string; + lossless: boolean; + encoded_bytes: number; + compression_ratio: number | null; +}; + +type Htj2kEncodeDemoManifest = { + format: string; + store: string; + image: { kind: string; shape: number[]; dtype: string }; + chunks: number[]; + multiscale_levels: number; + variants: Htj2kEncodeDemoVariant[]; +}; + +type MandelbulbFixtureManifest = { + format: string; + codec: string; + shape: number[]; + chunks: number[]; + image_path: string; +}; + +const FIXTURE_CONFIG: Record< + CodecFixtureKind, + { + label: string; + storeName: string; + getFixtureUrl: (origin?: string) => string; + getManifestUrl: (origin?: string) => string; + } +> = { + jpeg2k: { + label: 'JP2K', + storeName: 'jpeg2k.zarr', + getFixtureUrl: getLocalJpeg2kCodecFixtureUrl, + getManifestUrl: getLocalJpeg2kCodecManifestUrl, + }, + mandelbulb: { + label: 'HTJ2K Mandelbulb', + storeName: 'mandelbulb.zarr', + getFixtureUrl: getLocalMandelbulbCodecFixtureUrl, + getManifestUrl: getLocalMandelbulbCodecManifestUrl, + }, + htj2k: { + label: 'HTJ2K (experimental.openjph_htj2k)', + storeName: 'htj2k-demo.zarr', + getFixtureUrl: getLocalHtj2kEncodeDemoFixtureUrl, + getManifestUrl: getLocalHtj2kEncodeDemoManifestUrl, + }, +}; + +const panelStyle = { + flexShrink: 0, + padding: '10px 12px', + borderBottom: '1px solid #333', + background: '#1e1e1e', + fontSize: 12, +} as const; + +const selectStyle = { + background: '#2a2a2a', + color: '#eee', + border: '1px solid #444', + borderRadius: 4, + padding: '4px 8px', +} as const; + +const viewerShellStyle = { + flex: 1, + minHeight: 0, + position: 'relative' as const, +}; + +function formatBytes(bytes: number): string { + if (bytes < 1024) return `${bytes} B`; + if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(1)} KiB`; + return `${(bytes / (1024 * 1024)).toFixed(2)} MiB`; +} + +function HeadlessCodecFixtureViewer({ + fixtureKind, + fixtureUrl, + manifestUrl, +}: { + fixtureKind: CodecFixtureKind; + fixtureUrl: string; + manifestUrl: string; +}) { + const fixtureConfig = FIXTURE_CONFIG[fixtureKind]; + const { spatialData, loading, error } = useSpatialData(); + const coordinateSystems = useMemo(() => spatialData?.coordinateSystems ?? [], [spatialData]); + const [coordinateSystem, setCoordinateSystem] = useState(null); + const [layers, setLayers] = useState>({}); + const [layerOrder, setLayerOrder] = useState([]); + const [viewState, setViewState] = useState(null); + + useEffect(() => { + if (!spatialData || coordinateSystems.length === 0) { + return; + } + setCoordinateSystem((prev) => prev ?? coordinateSystems[0] ?? null); + }, [spatialData, coordinateSystems]); + + useEffect(() => { + if (!spatialData || !coordinateSystem) { + return; + } + const built = buildHeadlessLayersForCoordinateSystem(spatialData, coordinateSystem); + setLayers(built.layers); + setLayerOrder(built.layerOrder); + setViewState(null); + }, [spatialData, coordinateSystem]); + + const statusMessage = useMemo(() => { + if (loading) return `Loading ${fixtureConfig.label} codec fixture...`; + if (error) return `Failed to load ${fixtureConfig.label} fixture: ${error.message}`; + if (!spatialData) return 'No SpatialData loaded.'; + if (!coordinateSystem) return 'No coordinate system available.'; + if (layerOrder.length === 0) return 'No layers in this coordinate system.'; + return null; + }, [loading, error, spatialData, coordinateSystem, layerOrder.length, fixtureConfig.label]); + + return ( +
+
+
+ Codec fixture SpatialCanvasViewer - local {fixtureConfig.storeName} +
+
+ + Store + + + Manifest + + + Codec: {fixtureConfig.label} + + + Coordinate system: {coordinateSystem ?? '-'} + + + Layers: {layerOrder.length} + +
+ {error ? ( +
+ Generate fixtures with pnpm test:fixtures:generate:codecs. +
+ ) : null} +
+ +
+ {statusMessage ? ( +
+ {statusMessage} +
+ ) : ( + + )} +
+
+ ); +} + +function MandelbulbFixturePanel({ + fixtureUrl, + manifestUrl, + manifest, +}: { + fixtureUrl: string; + manifestUrl: string; + manifest: MandelbulbFixtureManifest | null; +}) { + const [t, c, z, height, width] = manifest?.shape ?? []; + + return ( +
+
+ Mandelbulb volume SpatialCanvas - local{' '} + {manifest?.image_path ?? 'images/mandelbulb'} + {manifest ? ( + <> + {' '} + · codec {manifest.codec} + + ) : null} +
+
+ + Store + + + Manifest + + {manifest ? ( + <> + + Shape:{' '} + + t={t} c={c} z={z} {width}×{height} + + + + Chunks: {manifest.chunks.join(', ')} + + + ) : null} +
+
+ Use the image layer panel to scrub t and z selections across the + encoded volume. +
+
+ ); +} + +function Htj2kEncodeDemoPanel({ + fixtureUrl, + manifestUrl, + htj2kDemo, +}: { + fixtureUrl: string; + manifestUrl: string; + htj2kDemo: Htj2kEncodeDemoManifest | null; +}) { + const imageShape = htj2kDemo?.image.shape; + const multiscaleLevels = htj2kDemo?.multiscale_levels; + + return ( +
+
+ HTJ2K encode demo SpatialCanvas - local {htj2kDemo?.store ?? 'htj2k-demo.zarr'} +
+
+ + Store + + + Manifest + + {imageShape ? ( + + Image: {imageShape.slice(-2).join('×')} + {multiscaleLevels != null ? ( + <> + {' '} + · {multiscaleLevels} scales + + ) : null} + + ) : null} + + Images: {htj2kDemo?.variants.length ?? '-'} + +
+ {htj2kDemo ? ( +
+ Toggle mandelbrot_* layers to compare HTJ2K presets (balanced{' '} + q=0.0002, small q=0.001). Interactive per-q{' '} + transcoding in the viewer is planned for a later pass. +
+ ) : null} + {htj2kDemo ? ( + + + + + + + + + + + {htj2kDemo.variants.map((variant) => ( + + + + + + + ))} + +
Image keyPresetEncodedRatio
+ {variant.image_key} + {variant.label}{formatBytes(variant.encoded_bytes)} + {variant.compression_ratio != null ? `${variant.compression_ratio.toFixed(1)}×` : '-'} +
+ ) : null} +
+ ); +} + +export default function CodecFixtureDemo() { + const [fixtureKind, setFixtureKind] = useState('jpeg2k'); + const [htj2kDemo, setHtj2kDemo] = useState(null); + const [htj2kDemoError, setHtj2kDemoError] = useState(null); + const [mandelbulbManifest, setMandelbulbManifest] = useState( + null + ); + const [mandelbulbManifestError, setMandelbulbManifestError] = useState(null); + + const fixtureConfig = FIXTURE_CONFIG[fixtureKind]; + + useEffect(() => { + if (fixtureKind !== 'htj2k') { + setHtj2kDemo(null); + setHtj2kDemoError(null); + } + if (fixtureKind !== 'mandelbulb') { + setMandelbulbManifest(null); + setMandelbulbManifestError(null); + } + if (fixtureKind !== 'htj2k' && fixtureKind !== 'mandelbulb') { + return; + } + + let cancelled = false; + const activeKind = fixtureKind; + const manifestUrl = + activeKind === 'htj2k' + ? getLocalHtj2kEncodeDemoManifestUrl() + : getLocalMandelbulbCodecManifestUrl(); + + fetch(manifestUrl) + .then(async (response) => { + if (!response.ok) { + throw new Error(`${response.status} ${response.statusText}`); + } + return await response.json(); + }) + .then((manifest) => { + if (cancelled) return; + if (activeKind === 'htj2k') { + setHtj2kDemo(manifest as Htj2kEncodeDemoManifest); + setHtj2kDemoError(null); + } else { + setMandelbulbManifest(manifest as MandelbulbFixtureManifest); + setMandelbulbManifestError(null); + } + }) + .catch((error: unknown) => { + if (cancelled) return; + const message = error instanceof Error ? error.message : String(error); + if (activeKind === 'htj2k') { + setHtj2kDemo(null); + setHtj2kDemoError(message); + } else { + setMandelbulbManifest(null); + setMandelbulbManifestError(message); + } + }); + return () => { + cancelled = true; + }; + }, [fixtureKind]); + + const fixtureUrl = useMemo(() => fixtureConfig.getFixtureUrl(), [fixtureConfig]); + const manifestUrl = useMemo(() => fixtureConfig.getManifestUrl(), [fixtureConfig]); + + return ( +
+
+ + {htj2kDemoError ? ( +
+ HTJ2K encode-demo manifest unavailable ({htj2kDemoError}). Run{' '} + pnpm test:fixtures:generate:codecs. +
+ ) : null} + {mandelbulbManifestError ? ( +
+ Mandelbulb manifest unavailable ({mandelbulbManifestError}). Run{' '} + pnpm test:fixtures:generate:codecs. +
+ ) : null} +
+ {fixtureKind === 'htj2k' ? ( + + +
+ +
+ + ) : fixtureKind === 'mandelbulb' ? ( + + +
+ +
+ + ) : ( + + + + )} +
+ ); +} diff --git a/packages/vis/demo/src/enableDemoWorkerChunkDecode.ts b/packages/vis/demo/src/enableDemoWorkerChunkDecode.ts new file mode 100644 index 00000000..372f6348 --- /dev/null +++ b/packages/vis/demo/src/enableDemoWorkerChunkDecode.ts @@ -0,0 +1,15 @@ +import { enableWorkerChunkDecode } from 'zarrextra/workers'; + +let enabled = false; + +/** Enable fizarrita worker decode once for all vis demo routes (Sketch, codec fixture, …). */ +export function ensureDemoWorkerChunkDecode() { + if (enabled || typeof Worker === 'undefined') { + return; + } + + enableWorkerChunkDecode({ + workerUrl: new URL('../../../zarrextra/src/workers/codec-worker.ts', import.meta.url), + }); + enabled = true; +} diff --git a/packages/vis/demo/src/fixtureUrls.ts b/packages/vis/demo/src/fixtureUrls.ts index 24da73d7..8930d18b 100644 --- a/packages/vis/demo/src/fixtureUrls.ts +++ b/packages/vis/demo/src/fixtureUrls.ts @@ -8,6 +8,63 @@ export const LOCAL_BLOBS_FIXTURE_VERSION = '0.7.2'; * to the fixture server (started alongside the demo on the host, default port 38473). */ export function getLocalBlobsFixtureUrl(origin?: string): string { - const base = origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); return `${base}/test-fixtures/v${LOCAL_BLOBS_FIXTURE_VERSION}/blobs.zarr`; } + +/** URL for the local JP2K codec fixture generated by `pnpm test:fixtures:generate:codecs`. */ +export function getLocalJpeg2kCodecFixtureUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/jpeg2k.zarr`; +} + +/** URL for the JP2K fixture manifest emitted by the Python reference writer. */ +export function getLocalJpeg2kCodecManifestUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/jpeg2k.manifest.json`; +} + +/** URL for the multi-z Mandelbulb HTJ2K fixture (`[2,1,8,128,128]`). */ +export function getLocalMandelbulbCodecFixtureUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/mandelbulb.zarr`; +} + +/** URL for the Mandelbulb fixture manifest. */ +export function getLocalMandelbulbCodecManifestUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/mandelbulb.manifest.json`; +} + +/** URL for the HTJ2K encode-demo manifest (multiscale Mandelbrot, several quality presets). */ +export function getLocalHtj2kEncodeDemoManifestUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/htj2k-encode-demo.manifest.json`; +} + +/** URL for the HTJ2K encode-demo store (several quality presets in one SpatialData object). */ +export function getLocalHtj2kEncodeDemoFixtureUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/htj2k-demo.zarr`; +} + +/** URL for the local HTJ2K codec fixture generated by `pnpm test:fixtures:generate:codecs`. */ +export function getLocalHtj2kCodecFixtureUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/htj2k.zarr`; +} + +/** URL for the HTJ2K fixture manifest emitted by the Python reference writer. */ +export function getLocalHtj2kCodecManifestUrl(origin?: string): string { + const base = + origin ?? (typeof window !== 'undefined' ? window.location.origin : 'http://127.0.0.1:5173'); + return `${base}/test-fixtures/codecs/htj2k.manifest.json`; +} diff --git a/packages/vis/demo/src/main.tsx b/packages/vis/demo/src/main.tsx index 100820ec..56fd1f67 100644 --- a/packages/vis/demo/src/main.tsx +++ b/packages/vis/demo/src/main.tsx @@ -1,8 +1,11 @@ import React from 'react'; import ReactDOM from 'react-dom/client'; import App from './App'; +import { ensureDemoWorkerChunkDecode } from './enableDemoWorkerChunkDecode'; import './index.css'; +ensureDemoWorkerChunkDecode(); + const root = document.getElementById('root'); if (!root) { throw new Error('Root element not found'); diff --git a/packages/vis/demo/tsconfig.json b/packages/vis/demo/tsconfig.json index dc813b1f..efe9c4ad 100644 --- a/packages/vis/demo/tsconfig.json +++ b/packages/vis/demo/tsconfig.json @@ -27,7 +27,8 @@ "@spatialdata/layers": ["../../layers/src/index.ts"], "@spatialdata/react": ["../../react/src/index.ts"], "@spatialdata/vis": ["../src/index.ts"], - "zarrextra": ["../../zarrextra/src/index.ts"] + "zarrextra": ["../../zarrextra/src/index.ts"], + "zarrextra/workers": ["../../zarrextra/src/workers/index.ts"] } }, "include": ["src"] diff --git a/packages/vis/package.json b/packages/vis/package.json index 4613eec6..c194dfd3 100644 --- a/packages/vis/package.json +++ b/packages/vis/package.json @@ -33,23 +33,25 @@ "zarrita": "catalog:" }, "dependencies": { + "@deck.gl/core": "catalog:", + "@hms-dbmi/viv": "catalog:", "@luma.gl/core": "catalog:", "@math.gl/core": "catalog:", "@spatialdata/avivatorish": "workspace:*", - "@spatialdata/layers": "workspace:*", "@spatialdata/core": "workspace:*", + "@spatialdata/layers": "workspace:*", "@spatialdata/react": "workspace:*", - "@vivjs/views": "catalog:", "@uidotdev/usehooks": "^2.4.1", "@uiw/react-json-view": "2.0.0-alpha.39", - "@deck.gl/core": "catalog:", - "@hms-dbmi/viv": "catalog:", + "@vivjs/views": "catalog:", "deck.gl": "catalog:", "fast-deep-equal": "^3.1.3", "geotiff": "2.1.4-beta.0", "zustand": "^5.0.8" }, "devDependencies": { + "@cornerstonejs/codec-openjpeg": "^1.3.0", + "@cornerstonejs/codec-openjph": "^2.4.7", "@types/node": "catalog:", "@types/react": "catalog:", "@types/react-dom": "catalog:", diff --git a/packages/vis/src/SpatialCanvas/VivLoaderRegistry.tsx b/packages/vis/src/SpatialCanvas/VivLoaderRegistry.tsx index 34e130f8..5e63c51d 100644 --- a/packages/vis/src/SpatialCanvas/VivLoaderRegistry.tsx +++ b/packages/vis/src/SpatialCanvas/VivLoaderRegistry.tsx @@ -1,9 +1,12 @@ -import { createContext, useContext, useMemo, type PropsWithChildren } from 'react'; -import { loadOmeZarrMultiscalesData } from '@spatialdata/avivatorish'; +import { + type OmeZarrMultiscalesSource, + loadOmeZarrMultiscalesData, +} from '@spatialdata/avivatorish'; +import { type PropsWithChildren, createContext, useContext, useMemo } from 'react'; export type VivLoaderRegistryValue = { - /** Multiscales pixel sources for an OME-Zarr URL (SpatialCanvas image path). */ - getOmeZarrMultiscalesData: (url: string) => Promise; + /** Multiscales pixel sources for an OME-Zarr store or URL (SpatialCanvas image path). */ + getOmeZarrMultiscalesData: (source: OmeZarrMultiscalesSource) => Promise; }; const defaultRegistry: VivLoaderRegistryValue = { @@ -16,10 +19,7 @@ export function VivLoaderRegistryProvider({ children, value, }: PropsWithChildren<{ value?: Partial }>) { - const merged = useMemo( - () => ({ ...defaultRegistry, ...value }), - [value?.getOmeZarrMultiscalesData] - ); + const merged = useMemo(() => ({ ...defaultRegistry, ...value }), [value]); return ( {children} ); diff --git a/packages/vis/src/SpatialCanvas/renderers/imageRenderer.ts b/packages/vis/src/SpatialCanvas/renderers/imageRenderer.ts index b27d32f2..66237210 100644 --- a/packages/vis/src/SpatialCanvas/renderers/imageRenderer.ts +++ b/packages/vis/src/SpatialCanvas/renderers/imageRenderer.ts @@ -5,8 +5,11 @@ * OME-Zarr and other multiscale image formats. */ -import { loadOmeZarrMultiscalesData } from '@spatialdata/avivatorish'; import type { Matrix4 } from '@math.gl/core'; +import { + type OmeZarrMultiscalesSource, + loadOmeZarrMultiscalesData, +} from '@spatialdata/avivatorish'; import type { ImageElement, LabelsElement } from '@spatialdata/core'; import type { Layer } from 'deck.gl'; @@ -61,13 +64,18 @@ export function extractChannelConfig(config: { channelsVisible: boolean[]; selections: Partial<{ z: number; c: number; t: number }>[]; } { - const defaults = { - colors: [[255, 255, 255]] as [number, number, number][], - contrastLimits: [[0, 65535]] as [number, number][], + const defaults: { + colors: [number, number, number][]; + contrastLimits: [number, number][]; + channelsVisible: boolean[]; + selections: Partial<{ z: number; c: number; t: number }>[]; + } = { + colors: [[255, 255, 255]], + contrastLimits: [[0, 65535]], channelsVisible: [true], // Don't provide default selections - they should be built from loader dimensions // TODO - fix types wrt optional entries - selections: [] as Partial<{ z: number; c: number; t: number }>[], + selections: [], }; if (!config.channels) { @@ -90,19 +98,25 @@ export function extractChannelConfig(config: { */ export async function createImageLoader( element: ImageElement | LabelsElement, - fetchMultiscales: (url: string) => Promise = loadOmeZarrMultiscalesData + fetchMultiscales: ( + source: OmeZarrMultiscalesSource + ) => Promise = loadOmeZarrMultiscalesData ): Promise { - if (!element.url) { + const store = element.getStore(); + + if (!store && !element.url) { throw new Error( - `SpatialCanvas currently requires a URL-backed raster source for '${element.path}'. ` + - 'Store-backed Viv loading is not implemented yet.' + `SpatialCanvas requires a store-backed or URL-backed raster source for '${element.path}'.` ); } try { - return await fetchMultiscales(element.url); + return await fetchMultiscales({ store, url: element.url }); } catch (error) { - console.error(`[ImageRenderer] Failed to create loader for ${element.url}:`, error); + console.error( + `[ImageRenderer] Failed to create loader for ${element.url ?? element.path}:`, + error + ); throw error; } } diff --git a/packages/vis/vite.config.demo.ts b/packages/vis/vite.config.demo.ts index 291727fa..6c5db8e9 100644 --- a/packages/vis/vite.config.demo.ts +++ b/packages/vis/vite.config.demo.ts @@ -15,13 +15,17 @@ export default defineConfig({ root: path.resolve(__dirname, 'demo'), plugins: [react()], resolve: { - alias: { + alias: [ ...createWorkspaceSourceAliases(workspaceRoot), - react: reactRoot, - 'react-dom': reactDomRoot, - }, + { find: 'react', replacement: reactRoot }, + { find: 'react-dom', replacement: reactDomRoot }, + ], dedupe: ['react', 'react-dom'], }, + worker: { + format: 'es', + }, + assetsInclude: ['**/*.wasm'], server: { host: '127.0.0.1', port: 5173, diff --git a/packages/zarrextra/README.md b/packages/zarrextra/README.md index d2e673e7..7b2532cd 100644 --- a/packages/zarrextra/README.md +++ b/packages/zarrextra/README.md @@ -6,6 +6,8 @@ This package provides helper functions and types for: - Parsing zarr store contents into a tree structure - Working with consolidated metadata - Serializing zarr tree structures +- Registering additional Zarrita codecs, including JP2K (`imagecodecs_jpeg2k`) +- Loading OME-Zarr multiscales from an existing Zarrita store for Viv-compatible viewers - Result type for explicit error handling ## Result Type @@ -39,3 +41,82 @@ if (result.ok) { ## API See the TypeScript definitions for full API documentation. + +## Codec registration + +`registerJpeg2kCodec()` registers decode support for the standard +`imagecodecs_jpeg2k` codec id from the Zarr codecs registry. The default decoder +uses the optional `@cornerstonejs/codec-openjpeg` package. + +```typescript +import { registerJpeg2kCodec } from 'zarrextra'; + +registerJpeg2kCodec(); +``` + +Applications can pass a custom decoder for alternate WASM loading or tests: + +```typescript +import OpenJPEGJS from '@cornerstonejs/codec-openjpeg/decode'; +import { createOpenJpegDecoder, registerJpeg2kCodec } from 'zarrextra'; + +registerJpeg2kCodec({ decoder: createOpenJpegDecoder(OpenJPEGJS) }); +``` + +`registerExperimentalHtj2kCodec()` registers decode for `experimental.openjph_htj2k` +(new writes) and legacy `experimental.imagecodecs_htj2k` fixtures. Keep datasets +using either id clearly labelled until there is community/registry alignment. + +```typescript +import OpenJPHJS from '@cornerstonejs/codec-openjph'; +import { createOpenJphDecoder, registerExperimentalHtj2kCodec } from 'zarrextra'; + +registerExperimentalHtj2kCodec({ decoder: createOpenJphDecoder(OpenJPHJS) }); +``` + +For offline encode (fixtures, recompress), use `encodeHtj2kPlane()` or +`createOpenJphEncoder()` from the same package. Python `spatialdata-codec-writer` +uses vendored OpenJPH WASM with a persistent Node worker pool; new stores use +codec id `experimental.openjph_htj2k`. + +```typescript +import { encodeHtj2kPlane } from 'zarrextra'; + +const plane = new Uint16Array(width * height); +// ... fill plane ... +const encoded = await encodeHtj2kPlane(plane, { width, height }, { + reversible: false, + quality: 75, +}); +``` + +## Worker-backed chunk decode (browser) + +JP2K and other codec work can block the main thread for a long time. For browser +apps, use the optional `zarrextra/workers` entry with +[`@fideus-labs/fizarrita`](https://www.npmjs.com/package/@fideus-labs/fizarrita) +to offload chunk decode to a Web Worker pool: + +```typescript +import { enableWorkerChunkDecode, disableWorkerChunkDecode } from 'zarrextra/workers'; + +enableWorkerChunkDecode(); +// ... load JP2K-backed SpatialData and render tiles ... +disableWorkerChunkDecode(); +``` + +This uses a thin custom codec worker that registers zarrextra image codecs +(including OpenJPEG for `imagecodecs_jpeg2k` and OpenJPH for experimental HTJ2K) +into `zarrita.registry` inside the worker before fizarrita's codec handler runs. Built-in zarrita codecs (bytes, zstd, +blosc, …) are also adapted to fizarrita's worker metadata shape via +`wrapZarrRegistryForFizarritaWorker()`. Main-thread `registerJpeg2kCodec()` is not +required for that path. + +| Context | Setup | +|---------|-------| +| Node / CI | `registerJpeg2kCodec()` / `registerExperimentalHtj2kCodec()` on the main thread | +| Browser | `enableWorkerChunkDecode()` from `zarrextra/workers` before loading JP2K or HTJ2K data | + +Optional dependencies: `@fideus-labs/fizarrita`, `@fideus-labs/worker-pool`, +`@cornerstonejs/codec-openjpeg`, and `@cornerstonejs/codec-openjph` (bundled into +the worker script). diff --git a/packages/zarrextra/package.json b/packages/zarrextra/package.json index 6dcfa620..e6bdcb3d 100644 --- a/packages/zarrextra/package.json +++ b/packages/zarrextra/package.json @@ -9,6 +9,10 @@ ".": { "types": "./dist/index.d.ts", "import": "./dist/index.js" + }, + "./workers": { + "types": "./dist/workers.d.ts", + "import": "./dist/workers.js" } }, "files": [ @@ -29,6 +33,8 @@ "zod": "catalog:" }, "devDependencies": { + "@fideus-labs/fizarrita": "^1.4.1", + "@fideus-labs/worker-pool": "^1.0.0", "@types/node": "catalog:", "typescript": "catalog:", "vite": "catalog:", @@ -40,5 +46,11 @@ "type": "git", "url": "https://github.com/Taylor-CCB-Group/SpatialData.js.git", "directory": "packages/zarrextra" + }, + "optionalDependencies": { + "@cornerstonejs/codec-openjpeg": "^1.3.0", + "@cornerstonejs/codec-openjph": "^2.4.7", + "@fideus-labs/fizarrita": "^1.4.1", + "@fideus-labs/worker-pool": "^1.0.0" } } diff --git a/packages/zarrextra/src/chunkDecode.ts b/packages/zarrextra/src/chunkDecode.ts new file mode 100644 index 00000000..87c5d891 --- /dev/null +++ b/packages/zarrextra/src/chunkDecode.ts @@ -0,0 +1,104 @@ +import * as zarr from 'zarrita'; +import type { WorkerPool } from '@fideus-labs/worker-pool'; +import type { ChunkCache, GetWorkerOptions } from '@fideus-labs/fizarrita'; + +export type ZarrGetOptions = { + signal?: AbortSignal; +}; + +export type FizarritaGetWorkerOptions = Pick< + GetWorkerOptions, + 'workerUrl' | 'useSharedArrayBuffer' | 'cache' +> & { + pool: WorkerPool; +}; + +export type ChunkDecodeBackend = + | { kind: 'main' } + | { + kind: 'fizarrita'; + pool: WorkerPool; + options?: Omit; + }; + +let chunkDecodeBackend: ChunkDecodeBackend = { kind: 'main' }; + +export function getChunkDecodeBackend(): ChunkDecodeBackend { + return chunkDecodeBackend; +} + +export function setChunkDecodeBackend(backend: ChunkDecodeBackend): void { + chunkDecodeBackend = backend; +} + +type GetWorkerFn = ( + arr: zarr.Array, + selection: Array | null, + options: FizarritaGetWorkerOptions +) => Promise>; + +let getWorkerImpl: GetWorkerFn | undefined; + +export function setFizarritaGetWorker(impl: GetWorkerFn): void { + getWorkerImpl = impl; +} + +function rejectOnAbort(promise: Promise, signal?: AbortSignal): Promise { + if (!signal) { + return promise; + } + if (signal.aborted) { + return Promise.reject(signal.reason ?? new DOMException('Aborted', 'AbortError')); + } + return new Promise((resolve, reject) => { + const onAbort = () => { + reject(signal.reason ?? new DOMException('Aborted', 'AbortError')); + }; + signal.addEventListener('abort', onAbort, { once: true }); + promise.then( + (value) => { + signal.removeEventListener('abort', onAbort); + resolve(value); + }, + (error: unknown) => { + signal.removeEventListener('abort', onAbort); + reject(error); + } + ); + }); +} + +export async function getZarrChunk( + arr: zarr.Array, + selection: Array, + opts?: ZarrGetOptions +): Promise> { + const backend = getChunkDecodeBackend(); + if (backend.kind === 'fizarrita') { + if (!getWorkerImpl) { + throw new Error( + 'Worker chunk decode is enabled but fizarrita getWorker is not loaded. ' + + 'Import from zarrextra/workers instead of setting the backend directly.' + ); + } + const result = await rejectOnAbort( + getWorkerImpl(arr, selection, { + pool: backend.pool, + workerUrl: backend.options?.workerUrl, + useSharedArrayBuffer: backend.options?.useSharedArrayBuffer, + cache: backend.options?.cache, + }), + opts?.signal + ); + if (typeof result !== 'object' || result === null || !('data' in result)) { + throw new Error('Expected chunk object from fizarrita getWorker().'); + } + return result as zarr.Chunk; + } + + const result = await zarr.get(arr, selection, opts); + if (typeof result !== 'object' || result === null || !('data' in result)) { + throw new Error('Expected chunk object from zarr.get().'); + } + return result as zarr.Chunk; +} diff --git a/packages/zarrextra/src/codecs.ts b/packages/zarrextra/src/codecs.ts new file mode 100644 index 00000000..d8ad3cb7 --- /dev/null +++ b/packages/zarrextra/src/codecs.ts @@ -0,0 +1,362 @@ +import * as zarr from 'zarrita'; + +type ChunkMetadata = { + dataType: D; + shape: number[]; + codecs: zarr.CodecMetadata[]; + fillValue: zarr.Scalar | null; +}; + +/** Chunk metadata from zarrita (camelCase) or fizarrita workers (snake_case). */ +type ChunkMetadataInput = Partial & { + data_type?: zarr.DataType; + chunk_shape?: number[]; + fill_value?: zarr.Scalar | null; +}; + +function normalizeChunkMetadata(meta: ChunkMetadataInput): ChunkMetadata { + const dataType = meta.dataType ?? meta.data_type; + const shape = meta.shape ?? meta.chunk_shape; + if (!dataType) { + throw new Error('Chunk metadata is missing dataType / data_type.'); + } + if (!shape) { + throw new Error('Chunk metadata is missing shape / chunk_shape.'); + } + return { + dataType, + shape, + codecs: meta.codecs ?? [], + fillValue: meta.fillValue ?? meta.fill_value ?? null, + }; +} + +type Codec = { + kind?: 'array_to_array' | 'array_to_bytes' | 'bytes_to_bytes'; + encode(data: unknown): Promise | Uint8Array; + decode(data: Uint8Array): Promise> | zarr.Chunk; +}; + +type CodecEntry = { + kind?: Codec['kind']; + fromConfig: (config: unknown, meta: ChunkMetadata) => Codec; +}; + +export type DecodedImageBytes = ArrayBuffer | ArrayBufferView; + +export type ImageCodecDecoder = ( + encoded: Uint8Array, + meta: ChunkMetadata, + config: unknown +) => Promise | DecodedImageBytes; + +export interface RegisterImageCodecOptions { + /** + * Override the codec ids registered into Zarrita's global registry. + * Defaults include the standard registry id and a pragmatic alias. + */ + ids?: string[]; + /** Custom decoder used by tests or applications with their own WASM loading. */ + decoder?: ImageCodecDecoder; + /** Optional Emscripten locateFile hook for bundled WASM decoders. */ + locateFile?: (path: string, prefix: string) => string; +} + +export type OpenJpegFactory = (opts?: { + locateFile?: RegisterImageCodecOptions['locateFile']; +}) => Promise> | Record; + +export type OpenJphFactory = (opts?: { + locateFile?: RegisterImageCodecOptions['locateFile']; +}) => Promise> | Record; + +/** Emscripten locateFile hook that resolves bundled codec WASM to a bundler URL. */ +export function createWasmLocateFile( + wasmUrl: string +): NonNullable { + return (path, _prefix) => (path.endsWith('.wasm') ? wasmUrl : path); +} + +const JPEG2K_CODEC_IDS = ['imagecodecs_jpeg2k', 'numcodecs.imagecodecs_jpeg2k', 'jpeg2k']; +const HTJ2K_OPENJPH_CODEC_ID = 'experimental.openjph_htj2k'; +const HTJ2K_LEGACY_CODEC_IDS = [ + 'experimental.imagecodecs_htj2k', + 'imagecodecs_htj2k', + 'numcodecs.imagecodecs_htj2k', +]; +const HTJ2K_CODEC_IDS = [HTJ2K_OPENJPH_CODEC_ID, ...HTJ2K_LEGACY_CODEC_IDS]; + +const dynamicImport = new Function('specifier', 'return import(specifier)') as ( + specifier: string +) => Promise>; + +function unsupportedEncode(codecName: string): never { + throw new Error(`${codecName} encode is not implemented in zarrextra; decode-only for now.`); +} + +function toUint8Array(data: DecodedImageBytes): Uint8Array { + if (data instanceof Uint8Array) { + return data; + } + if (ArrayBuffer.isView(data)) { + return new Uint8Array(data.buffer, data.byteOffset, data.byteLength); + } + return new Uint8Array(data); +} + +function copyArrayBufferView(bytes: Uint8Array): ArrayBuffer { + const copy = new ArrayBuffer(bytes.byteLength); + new Uint8Array(copy).set(bytes); + return copy; +} + +function product(values: number[]): number { + return values.reduce((acc, value) => acc * value, 1); +} + +function getStrides(shape: number[]): number[] { + const stride = new Array(shape.length); + let step = 1; + for (let index = shape.length - 1; index >= 0; index -= 1) { + stride[index] = step; + step *= shape[index] ?? 1; + } + return stride; +} + +function typedArrayFromDecodedBytes( + decoded: DecodedImageBytes, + meta: ChunkMetadata +): zarr.TypedArray { + if (Array.isArray(decoded)) { + throw new Error('Image codec decoder returned a plain array; expected binary data.'); + } + + const decodedBytes = toUint8Array(decoded); + const buffer = copyArrayBufferView(decodedBytes); + const expectedValues = product(meta.shape); + + let data: zarr.TypedArray; + switch (meta.dataType) { + case 'uint8': + data = new Uint8Array(buffer); + break; + case 'int8': + data = new Int8Array(buffer); + break; + case 'uint16': + data = new Uint16Array(buffer); + break; + case 'int16': + data = new Int16Array(buffer); + break; + case 'uint32': + data = new Uint32Array(buffer); + break; + case 'int32': + data = new Int32Array(buffer); + break; + case 'float32': + data = new Float32Array(buffer); + break; + case 'float64': + data = new Float64Array(buffer); + break; + default: + throw new Error(`Image codec does not support Zarrita dtype '${meta.dataType}'.`); + } + + if (data.length !== expectedValues) { + throw new Error( + `Image codec decoded ${data.length} values, expected ${expectedValues} for chunk shape ` + + `[${meta.shape.join(', ')}].` + ); + } + + return data; +} + +function createImageCodecEntry( + codecName: string, + decoder: ImageCodecDecoder +): () => Promise { + return async () => ({ + kind: 'array_to_bytes', + fromConfig(config: unknown, meta: ChunkMetadataInput): Codec { + const chunkMeta = normalizeChunkMetadata(meta); + return { + kind: 'array_to_bytes', + encode: () => unsupportedEncode(codecName), + async decode(encoded: Uint8Array) { + const decoded = await decoder(encoded, chunkMeta, config); + return { + data: typedArrayFromDecodedBytes(decoded, chunkMeta), + shape: chunkMeta.shape, + stride: getStrides(chunkMeta.shape), + }; + }, + }; + }, + }); +} + +/** + * Adapt zarrita's built-in registry codecs for fizarrita's worker metadata + * (`data_type`, `chunk_shape`) before fizarrita's codec worker loads. + */ +export function wrapZarrRegistryForFizarritaWorker() { + const { registry } = zarr; + for (const [id, factory] of [...registry.entries()]) { + registry.set(id, async () => { + const entry = await factory(); + if (typeof entry.fromConfig !== 'function') { + return entry; + } + const fromConfig = entry.fromConfig.bind(entry); + return { + ...entry, + fromConfig(config: unknown, meta: ChunkMetadataInput) { + return fromConfig(config, normalizeChunkMetadata(meta)); + }, + }; + }); + } +} + +export function createOpenJpegDecoder( + factory: OpenJpegFactory, + options: Pick = {} +): ImageCodecDecoder { + let runtimePromise: Promise> | undefined; + async function getRuntime() { + runtimePromise ??= Promise.resolve( + factory({ + locateFile: options.locateFile, + }) + ); + return await runtimePromise; + } + return async (encoded) => { + const runtime = await getRuntime(); + const Decoder = runtime.J2KDecoder as + | (new () => { + getEncodedBuffer(length: number): Uint8Array; + decode(): void; + getDecodedBuffer(): DecodedImageBytes; + }) + | undefined; + if (!Decoder) { + throw new Error('OpenJPEG runtime does not expose J2KDecoder.'); + } + const decoder = new Decoder(); + decoder.getEncodedBuffer(encoded.length).set(encoded); + decoder.decode(); + return decoder.getDecodedBuffer(); + }; +} + +async function loadOpenJpegDecoder(options: RegisterImageCodecOptions): Promise { + const mod = await dynamicImport('@cornerstonejs/codec-openjpeg/decode').catch(() => + dynamicImport('@cornerstonejs/codec-openjpeg') + ); + const factory = (mod.default ?? mod.OpenJPEGJS ?? mod.OpenJPEGWASM ?? mod) as unknown; + if (typeof factory !== 'function') { + throw new Error('Could not find an OpenJPEG factory export in @cornerstonejs/codec-openjpeg.'); + } + return createOpenJpegDecoder(factory as OpenJpegFactory, options); +} + +type Htj2kDecoderClass = new () => { + getEncodedBuffer(length: number): Uint8Array; + decode(): void; + getDecodedBuffer(): DecodedImageBytes; +}; + +export function createOpenJphDecoder( + factory: OpenJphFactory, + options: Pick = {} +): ImageCodecDecoder { + let runtimePromise: Promise> | undefined; + async function getRuntime() { + runtimePromise ??= Promise.resolve( + factory({ + locateFile: options.locateFile, + }) + ); + return await runtimePromise; + } + return async (encoded) => { + const runtime = await getRuntime(); + const Decoder = (runtime.HTJ2KDecoder ?? runtime.JPHDecoder ?? runtime.J2KDecoder) as + | Htj2kDecoderClass + | undefined; + if (!Decoder) { + throw new Error( + 'OpenJPH runtime does not expose a known decoder class; pass a custom decoder option.' + ); + } + const decoder = new Decoder(); + decoder.getEncodedBuffer(encoded.length).set(encoded); + decoder.decode(); + return decoder.getDecodedBuffer(); + }; +} + +async function loadOpenJphDecoder(options: RegisterImageCodecOptions): Promise { + const factoryMod = await dynamicImport('@cornerstonejs/codec-openjph/wasmjs').catch(() => + dynamicImport('@cornerstonejs/codec-openjph') + ); + const factory = (factoryMod.default ?? factoryMod.OpenJPHJS ?? factoryMod) as unknown; + if (typeof factory !== 'function') { + throw new Error('Could not find an OpenJPH factory export in @cornerstonejs/codec-openjph.'); + } + const wasmMod = await dynamicImport('@cornerstonejs/codec-openjph/wasm').catch(() => null); + const wasmAsset = wasmMod ? ((wasmMod.default ?? wasmMod) as string | undefined) : undefined; + const locateFile = + options.locateFile ?? (wasmAsset ? createWasmLocateFile(wasmAsset) : undefined); + return createOpenJphDecoder(factory as OpenJphFactory, { locateFile }); +} + +function registerImageCodec( + codecName: string, + defaultIds: string[], + defaultDecoder: (options: RegisterImageCodecOptions) => Promise, + options: RegisterImageCodecOptions = {} +) { + const ids = options.ids ?? defaultIds; + let decoderPromise: Promise | undefined; + const getDecoder = async () => { + decoderPromise ??= Promise.resolve(options.decoder ?? defaultDecoder(options)); + return await decoderPromise; + }; + + for (const id of ids) { + (zarr.registry as Map Promise>).set( + id, + createImageCodecEntry(codecName, async (encoded, meta, config) => { + const decoder = await getDecoder(); + return await decoder(encoded, meta, config); + }) + ); + } +} + +/** Register decode support for the standard `imagecodecs_jpeg2k` Zarr codec id. */ +export function registerJpeg2kCodec(options: RegisterImageCodecOptions = {}) { + registerImageCodec('imagecodecs_jpeg2k', JPEG2K_CODEC_IDS, loadOpenJpegDecoder, options); +} + +/** + * Register HTJ2K decode support for OpenJPH-encoded stores and legacy ids. + * + * New writes use `experimental.openjph_htj2k`. Older fixtures may use + * `experimental.imagecodecs_htj2k`; both decode through the same OpenJPH WASM path. + */ +export function registerExperimentalHtj2kCodec(options: RegisterImageCodecOptions = {}) { + registerImageCodec( + HTJ2K_OPENJPH_CODEC_ID, + HTJ2K_CODEC_IDS, + loadOpenJphDecoder, + options + ); +} diff --git a/packages/zarrextra/src/htj2k-encode.ts b/packages/zarrextra/src/htj2k-encode.ts new file mode 100644 index 00000000..b497cedd --- /dev/null +++ b/packages/zarrextra/src/htj2k-encode.ts @@ -0,0 +1,155 @@ +import { createWasmLocateFile, type OpenJphFactory, type RegisterImageCodecOptions } from './codecs'; + +export type Htj2kPlaneDtype = 'uint8' | 'int8' | 'uint16' | 'int16'; + +export type Htj2kEncodeOptions = { + /** Lossless when true. Defaults to true for fixture-style writes. */ + reversible?: boolean; + /** OpenJPH quantization factor when irreversible (lower = higher fidelity, larger output). */ + quality?: number; + locateFile?: RegisterImageCodecOptions['locateFile']; +}; + +type Htj2kFrameInfo = { + width: number; + height: number; + bitsPerSample: 8 | 16; + isSigned: boolean; + componentCount: 1; + isUsingColorTransform: false; +}; + +type Htj2kEncoderClass = new () => { + /** OpenJPH WASM API: `setQuality(reversible, quality)`; quality is a quantization factor (lower = better). */ + setQuality(reversible: boolean, quality: number): void; + getDecodedBuffer(frame: Htj2kFrameInfo): ArrayBufferView; + encode(): void; + getEncodedBuffer(): Uint8Array; +}; + +export type OpenJphEncoder = ( + plane: Uint8Array | Uint16Array | Int8Array | Int16Array, + size: { width: number; height: number }, + options?: Pick +) => Promise; + +const dynamicImport = new Function('specifier', 'return import(specifier)') as ( + specifier: string +) => Promise>; + +function bitsPerSampleForPlane( + plane: Uint8Array | Uint16Array | Int8Array | Int16Array +): 8 | 16 { + return plane instanceof Uint16Array || plane instanceof Int16Array ? 16 : 8; +} + +function isSignedPlane(plane: Uint8Array | Uint16Array | Int8Array | Int16Array): boolean { + return plane instanceof Int8Array || plane instanceof Int16Array; +} + +function frameInfoForPlane( + plane: Uint8Array | Uint16Array | Int8Array | Int16Array, + size: { width: number; height: number } +): Htj2kFrameInfo { + const { width, height } = size; + const expectedValues = width * height; + if (plane.length !== expectedValues) { + throw new Error( + `HTJ2K plane has ${plane.length} samples, expected ${expectedValues} for ${width}x${height}.` + ); + } + return { + width, + height, + bitsPerSample: bitsPerSampleForPlane(plane), + isSigned: isSignedPlane(plane), + componentCount: 1, + isUsingColorTransform: false, + }; +} + +/** Create an HTJ2K encoder backed by an OpenJPH WASM factory. */ +export function createOpenJphEncoder( + factory: OpenJphFactory, + options: Pick = {} +): OpenJphEncoder { + let runtimePromise: Promise> | undefined; + + async function getRuntime() { + runtimePromise ??= Promise.resolve( + factory({ + locateFile: options.locateFile, + }) + ); + return await runtimePromise; + } + + return async (plane, size, encodeOptions = {}) => { + const runtime = await getRuntime(); + const Encoder = runtime.HTJ2KEncoder as Htj2kEncoderClass | undefined; + if (!Encoder) { + throw new Error('OpenJPH runtime does not expose HTJ2KEncoder.'); + } + + const reversible = encodeOptions.reversible ?? true; + const quality = encodeOptions.quality ?? 0; + const frame = frameInfoForPlane(plane, size); + const encoder = new Encoder(); + encoder.setQuality(reversible, quality); + + const buffer = encoder.getDecodedBuffer(frame); + const target = + frame.bitsPerSample === 16 + ? new Uint16Array(buffer.buffer, buffer.byteOffset, plane.length) + : new Uint8Array(buffer.buffer, buffer.byteOffset, plane.length); + target.set(plane); + encoder.encode(); + return encoder.getEncodedBuffer(); + }; +} + +/** Load the optional OpenJPH WASM encoder from @cornerstonejs/codec-openjph. */ +export async function loadOpenJphEncoder( + options: Htj2kEncodeOptions = {} +): Promise { + const factoryMod = await dynamicImport('@cornerstonejs/codec-openjph/wasmjs').catch(() => + dynamicImport('@cornerstonejs/codec-openjph') + ); + const factory = (factoryMod.default ?? factoryMod.OpenJPHJS ?? factoryMod) as unknown; + if (typeof factory !== 'function') { + throw new Error('Could not find an OpenJPH factory export in @cornerstonejs/codec-openjph.'); + } + const wasmMod = await dynamicImport('@cornerstonejs/codec-openjph/wasm').catch(() => null); + const wasmAsset = wasmMod ? ((wasmMod.default ?? wasmMod) as string | undefined) : undefined; + const locateFile = + options.locateFile ?? (wasmAsset ? createWasmLocateFile(wasmAsset) : undefined); + return createOpenJphEncoder(factory as OpenJphFactory, { locateFile }); +} + +export function planeArrayForDtype( + dtype: Htj2kPlaneDtype, + bytes: Uint8Array +) { + switch (dtype) { + case 'uint8': + return bytes; + case 'int8': + return new Int8Array(bytes.buffer, bytes.byteOffset, bytes.byteLength); + case 'uint16': + return new Uint16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + case 'int16': + return new Int16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + default: + throw new Error(`Unsupported HTJ2K plane dtype '${dtype}'.`); + } +} + +/** Encode one 2D plane to an HTJ2K bitstream. */ +export async function encodeHtj2kPlane( + plane: Uint8Array | Uint16Array | Int8Array | Int16Array, + size: { width: number; height: number }, + options: Htj2kEncodeOptions = {} +): Promise { + const encoder = await loadOpenJphEncoder(options); + return await encoder(plane, size, options); +} diff --git a/packages/zarrextra/src/index.ts b/packages/zarrextra/src/index.ts index 07ae85d6..d143868a 100644 --- a/packages/zarrextra/src/index.ts +++ b/packages/zarrextra/src/index.ts @@ -1,13 +1,13 @@ import * as zarr from 'zarrita'; +import { Err, Ok, type Result } from './result'; import type { ConsolidatedStore, LazyZarrArray, StoreReference, - ZarrTree, ZAttrsAny, + ZarrTree, } from './types'; import { ATTRS_KEY, ZARRAY_KEY } from './types'; -import { Err, Ok, type Result } from './result'; const decoder = new TextDecoder(); @@ -204,6 +204,32 @@ export type { ZAttrsAny, } from './types'; export { ATTRS_KEY, ZARRAY_KEY } from './types'; +export { createPrefixedStore } from './prefixedStore'; +export { + createOpenJpegDecoder, + createOpenJphDecoder, + createWasmLocateFile, + registerJpeg2kCodec, + registerExperimentalHtj2kCodec, + type ImageCodecDecoder, + type OpenJpegFactory, + type OpenJphFactory, + type RegisterImageCodecOptions, +} from './codecs'; +export { + createOpenJphEncoder, + encodeHtj2kPlane, + loadOpenJphEncoder, + planeArrayForDtype, + type Htj2kEncodeOptions, + type Htj2kPlaneDtype, + type OpenJphEncoder, +} from './htj2k-encode'; +export { + loadOmeZarrMultiscalesFromStore, + type VivCompatiblePixelSource, + type RasterSelection, +} from './omeZarr'; export type { Result } from './result'; export { Ok, Err, isOk, isErr, unwrap, unwrapOr } from './result'; diff --git a/packages/zarrextra/src/omeZarr.ts b/packages/zarrextra/src/omeZarr.ts new file mode 100644 index 00000000..96843077 --- /dev/null +++ b/packages/zarrextra/src/omeZarr.ts @@ -0,0 +1,317 @@ +import * as zarr from 'zarrita'; +import { getZarrChunk } from './chunkDecode'; + +export type RasterSelection = Record | number[]; + +export interface VivCompatiblePixelSource { + labels: string[]; + tileSize: number; + shape: number[]; + dtype: string; + meta?: { physicalSizes?: { x?: { size: number; unit: string } } }; + getRaster(props: { selection: RasterSelection; signal?: AbortSignal }): Promise<{ + data: unknown; + width: number; + height: number; + }>; + getTile(props: { + x: number; + y: number; + selection: RasterSelection; + signal?: AbortSignal; + }): Promise<{ + data: unknown; + width: number; + height: number; + }>; + onTileError(err: Error): void; +} + +type OmeAxis = { name: string; type?: string; unit?: string }; +type OmeMultiscaleAttrs = { + datasets?: Array<{ path: string }>; + axes?: Array; +}; +type OmeRootAttrs = { + multiscales?: OmeMultiscaleAttrs[]; + omero?: unknown; + [key: string]: unknown; +}; + +function isObject(value: unknown): value is Record { + return typeof value === 'object' && value !== null && !Array.isArray(value); +} + +function isOmeAxis(value: unknown): value is OmeAxis { + return isObject(value) && typeof value.name === 'string'; +} + +function isOmeDataset(value: unknown): value is { path: string } { + return isObject(value) && typeof value.path === 'string'; +} + +function isOmeMultiscaleAttrs(value: unknown): value is OmeMultiscaleAttrs { + if (!isObject(value)) return false; + const datasets = value.datasets; + if (datasets !== undefined) { + if (!Array.isArray(datasets)) return false; + if (!datasets.every(isOmeDataset)) return false; + } + const axes = value.axes; + if (axes !== undefined) { + if (!Array.isArray(axes)) return false; + if (!axes.every((axis) => typeof axis === 'string' || isOmeAxis(axis))) return false; + } + return true; +} + +function getOmeRootAttrs(attrs: Record): OmeRootAttrs { + const candidate = isObject(attrs.ome) ? attrs.ome : attrs; + if (!('multiscales' in candidate)) { + return candidate; + } + if (!Array.isArray(candidate.multiscales)) { + throw new Error('OME-Zarr `multiscales` attribute must be an array.'); + } + if (!candidate.multiscales.every(isOmeMultiscaleAttrs)) { + throw new Error('OME-Zarr `multiscales` entries must contain valid dataset paths and axes.'); + } + return candidate; +} + +function isInterleaved(shape: number[], labels?: string[]) { + const lastDimSize = shape[shape.length - 1]; + if (lastDimSize !== 3 && lastDimSize !== 4) { + return false; + } + if (labels?.some((label) => label.toLowerCase() === 'c')) { + return false; + } + return true; +} + +function axisIndex(labels: string[], axis: 'x' | 'y'): number { + const index = labels.findIndex((label) => label.toLowerCase() === axis); + if (index === -1) { + throw new Error(`OME-Zarr labels must include '${axis}' axis.`); + } + return index; +} + +function spatialAxisIndices(shape: number[], labels: string[]): { xIndex: number; yIndex: number } { + if (isInterleaved(shape, labels)) { + const len = shape.length; + return { yIndex: len - 3, xIndex: len - 2 }; + } + return { yIndex: axisIndex(labels, 'y'), xIndex: axisIndex(labels, 'x') }; +} + +function spatialDimensions(shape: number[], labels: string[]): [number, number] { + const { xIndex, yIndex } = spatialAxisIndices(shape, labels); + return [shape[yIndex] ?? 0, shape[xIndex] ?? 0]; +} + +function spatialDimensionsFromChunk( + chunkShape: number[], + sourceShape: number[], + labels: string[] +): [number, number] { + if (isInterleaved(sourceShape, labels)) { + const [height, width] = chunkShape.slice(-3); + return [height ?? 0, width ?? 0]; + } + if (chunkShape.length >= 2) { + const [height, width] = chunkShape.slice(-2); + return [height ?? 0, width ?? 0]; + } + return [chunkShape[0] ?? 0, 0]; +} + +function getImageSize(source: { shape: number[]; labels: string[] }) { + const [height, width] = spatialDimensions(source.shape, source.labels); + return { height, width }; +} + +function prevPowerOf2(x: number): number { + return 2 ** Math.floor(Math.log2(x)); +} + +function guessTileSize(arr: zarr.Array, labels: string[]): number { + if (isInterleaved(arr.shape, labels)) { + const [yChunk, xChunk] = arr.chunks.slice(-3); + return prevPowerOf2(Math.min(yChunk ?? 1, xChunk ?? 1)); + } + const yChunk = arr.chunks[axisIndex(labels, 'y')]; + const xChunk = arr.chunks[axisIndex(labels, 'x')]; + return prevPowerOf2(Math.min(yChunk ?? 1, xChunk ?? 1)); +} + +function labelsFromAxes(axes: OmeMultiscaleAttrs['axes'] | undefined): string[] { + if (!axes) return ['t', 'c', 'z', 'y', 'x']; + return axes.map((axis) => (typeof axis === 'string' ? axis : axis.name)); +} + +function normalizeDtype(dtype: string): string { + const lookup: Record = { + u1: 'Uint8', + u2: 'Uint16', + u4: 'Uint32', + i1: 'Int8', + i2: 'Int16', + i4: 'Int32', + f4: 'Float32', + f8: 'Float64', + uint8: 'Uint8', + uint16: 'Uint16', + uint32: 'Uint32', + int8: 'Int8', + int16: 'Int16', + int32: 'Int32', + float32: 'Float32', + float64: 'Float64', + }; + return lookup[dtype.toLowerCase()] ?? dtype.charAt(0).toUpperCase() + dtype.slice(1); +} + +function getIndexer(labels: string[]) { + const labelSet = new Set(labels); + if (labelSet.size !== labels.length) { + throw new Error('OME-Zarr labels must be unique.'); + } + return (selection: RasterSelection): Array => { + if (Array.isArray(selection)) { + return [...selection]; + } + const indexed: Array = Array(labels.length).fill(0); + for (const [key, value] of Object.entries(selection)) { + const index = labels.indexOf(key); + if (index === -1) { + throw new Error(`Invalid OME-Zarr selection axis '${key}'.`); + } + indexed[index] = value; + } + return indexed; + }; +} + +class BoundsCheckError extends Error {} + +class ZarrPixelSource implements VivCompatiblePixelSource { + private readonly indexer: ReturnType; + + constructor( + private readonly data: zarr.Array, + public readonly labels: string[], + public readonly tileSize: number + ) { + this.indexer = getIndexer(labels); + } + + get shape() { + return this.data.shape; + } + + get dtype() { + return normalizeDtype(this.data.dtype); + } + + private chunkIndex( + selection: RasterSelection, + tile: { x: number | zarr.Slice | null; y: number | zarr.Slice | null } + ) { + const { xIndex, yIndex } = spatialAxisIndices(this.data.shape, this.labels); + const sel = this.indexer(selection); + sel[xIndex] = tile.x; + sel[yIndex] = tile.y; + return sel; + } + + private getSlices(x: number, y: number) { + const { height, width } = getImageSize(this); + const xStart = x * this.tileSize; + const xStop = Math.min((x + 1) * this.tileSize, width); + const yStart = y * this.tileSize; + const yStop = Math.min((y + 1) * this.tileSize, height); + + if (xStart >= xStop || yStart >= yStop) { + throw new BoundsCheckError('Tile slice is zero-sized or inverted.'); + } + if (xStart < 0 || yStart < 0 || xStop > width || yStop > height) { + throw new BoundsCheckError('Tile slice is out of bounds.'); + } + + return [zarr.slice(xStart, xStop), zarr.slice(yStart, yStop)]; + } + + private async getRaw( + selection: Array, + signal?: AbortSignal + ): Promise> { + return await getZarrChunk(this.data, selection, { signal }); + } + + async getRaster({ selection, signal }: { selection: RasterSelection; signal?: AbortSignal }) { + const sel = this.chunkIndex(selection, { x: null, y: null }); + const result = await this.getRaw(sel, signal); + const [height, width] = spatialDimensionsFromChunk( + result.shape, + this.data.shape, + this.labels + ); + return { data: result.data, width, height }; + } + + async getTile({ + x, + y, + selection, + signal, + }: { + x: number; + y: number; + selection: RasterSelection; + signal?: AbortSignal; + }) { + const [xSlice, ySlice] = this.getSlices(x, y); + const sel = this.chunkIndex(selection, { x: xSlice, y: ySlice }); + const result = await this.getRaw(sel, signal); + const [height, width] = spatialDimensionsFromChunk( + result.shape, + this.data.shape, + this.labels + ); + return { data: result.data, width, height }; + } + + onTileError(err: Error) { + if (!(err instanceof BoundsCheckError)) { + throw err; + } + } +} + +async function loadMultiscales(store: zarr.AsyncReadable) { + const readable = await zarr.withMaybeConsolidatedMetadata(store); + const root = zarr.root(readable); + const group = await zarr.open(root, { kind: 'group' }); + const rootAttrs = getOmeRootAttrs(group.attrs); + const firstMultiscale = rootAttrs.multiscales?.[0]; + const paths: string[] = firstMultiscale?.datasets?.map((dataset) => dataset.path) ?? ['0']; + const labels = labelsFromAxes(firstMultiscale?.axes); + const data: Array> = await Promise.all( + paths.map((path: string) => zarr.open(root.resolve(path), { kind: 'array' })) + ); + return { data, labels, rootAttrs }; +} + +/** Load an OME-Zarr multiscale image from a Zarrita readable store. */ +export async function loadOmeZarrMultiscalesFromStore( + store: zarr.AsyncReadable +): Promise { + const { data, labels } = await loadMultiscales(store); + if (data.length === 0) { + throw new Error('OME-Zarr multiscale dataset is empty or has no valid arrays.'); + } + const tileSize = guessTileSize(data[0], labels); + return data.map((arr: zarr.Array) => new ZarrPixelSource(arr, labels, tileSize)); +} diff --git a/packages/zarrextra/src/prefixedStore.ts b/packages/zarrextra/src/prefixedStore.ts new file mode 100644 index 00000000..cbb59258 --- /dev/null +++ b/packages/zarrextra/src/prefixedStore.ts @@ -0,0 +1,37 @@ +import type * as zarr from 'zarrita'; + +function toAbsolutePath(path: string): zarr.AbsolutePath { + const trimmed = path.replace(/^\/+|\/+$/g, ''); + // Zarrita brands absolute paths as template-literal types; normalization above enforces it. + return (trimmed ? `/${trimmed}` : '/') as zarr.AbsolutePath; +} + +function joinAbsolutePath(prefix: string, key: zarr.AbsolutePath): zarr.AbsolutePath { + const normalizedPrefix = toAbsolutePath(prefix); + if (normalizedPrefix === '/') { + return key; + } + if (key === '/') { + return normalizedPrefix; + } + // Both sides are absolute Zarr paths; concatenating preserves the leading slash. + return `${normalizedPrefix}${key}` as zarr.AbsolutePath; +} + +/** + * Create a read-only store view rooted at `prefix`. + * + * This is useful when callers have a SpatialData root store but a downstream + * reader expects the supplied store root to be an individual image/table group. + */ +export function createPrefixedStore(store: zarr.Readable, prefix: string): zarr.AsyncReadable { + return { + async get(key: zarr.AbsolutePath, opts?: zarr.GetOptions) { + return await store.get(joinAbsolutePath(prefix, key), opts); + }, + getRange: store.getRange + ? async (key: zarr.AbsolutePath, range: zarr.RangeQuery, opts?: zarr.GetOptions) => + await store.getRange?.(joinAbsolutePath(prefix, key), range, opts) + : undefined, + }; +} diff --git a/packages/zarrextra/src/workers/codec-worker-init.ts b/packages/zarrextra/src/workers/codec-worker-init.ts new file mode 100644 index 00000000..340da3e0 --- /dev/null +++ b/packages/zarrextra/src/workers/codec-worker-init.ts @@ -0,0 +1,24 @@ +import OpenJPHJS from '@cornerstonejs/codec-openjph'; +import openJphWasmUrl from '@cornerstonejs/codec-openjph/wasm?url'; +import OpenJPEGJS from '@cornerstonejs/codec-openjpeg/decode'; +import openJpegWasmUrl from '@cornerstonejs/codec-openjpeg/decodewasm?url'; +import { + createOpenJpegDecoder, + createOpenJphDecoder, + createWasmLocateFile, + registerExperimentalHtj2kCodec, + registerJpeg2kCodec, + wrapZarrRegistryForFizarritaWorker, +} from '../codecs'; + +wrapZarrRegistryForFizarritaWorker(); +registerJpeg2kCodec({ + decoder: createOpenJpegDecoder(OpenJPEGJS, { + locateFile: createWasmLocateFile(openJpegWasmUrl), + }), +}); +registerExperimentalHtj2kCodec({ + decoder: createOpenJphDecoder(OpenJPHJS, { + locateFile: createWasmLocateFile(openJphWasmUrl), + }), +}); diff --git a/packages/zarrextra/src/workers/codec-worker.ts b/packages/zarrextra/src/workers/codec-worker.ts new file mode 100644 index 00000000..e177a86a --- /dev/null +++ b/packages/zarrextra/src/workers/codec-worker.ts @@ -0,0 +1,5 @@ +// Registration must run before fizarrita's codec-worker installs message handlers. +// Use ordered static imports (not top-level await) so the worker is synchronously +// ready when the browser marks the script as loaded. +import './codec-worker-init'; +import '@fideus-labs/fizarrita/codec-worker'; diff --git a/packages/zarrextra/src/workers/index.ts b/packages/zarrextra/src/workers/index.ts new file mode 100644 index 00000000..92924d53 --- /dev/null +++ b/packages/zarrextra/src/workers/index.ts @@ -0,0 +1,61 @@ +import { WorkerPool } from '@fideus-labs/worker-pool'; +import { getWorker, type ChunkCache, type GetWorkerOptions } from '@fideus-labs/fizarrita'; +import { setChunkDecodeBackend, setFizarritaGetWorker } from '../chunkDecode'; + +export type { ChunkCache } from '@fideus-labs/fizarrita'; + +export type EnableWorkerChunkDecodeOptions = { + workers?: number; + workerUrl?: string | URL; + useSharedArrayBuffer?: boolean; + cache?: ChunkCache; +}; + +let activePool: WorkerPool | undefined; + +function defaultWorkerCount() { + if (typeof navigator !== 'undefined' && navigator.hardwareConcurrency) { + return Math.min(navigator.hardwareConcurrency, 4); + } + return 4; +} + +function defaultWorkerUrl() { + return new URL('./codec-worker.js', import.meta.url); +} + +setFizarritaGetWorker(getWorker); + +/** Enable fizarrita worker-pool chunk decode for all subsequent getZarrChunk reads. */ +export function enableWorkerChunkDecode(options: EnableWorkerChunkDecodeOptions = {}) { + if (activePool) { + disableWorkerChunkDecode(); + } + + const pool = new WorkerPool(options.workers ?? defaultWorkerCount()); + activePool = pool; + + const workerUrl = options.workerUrl ?? defaultWorkerUrl(); + setChunkDecodeBackend({ + kind: 'fizarrita', + pool, + options: { + workerUrl, + useSharedArrayBuffer: options.useSharedArrayBuffer, + cache: options.cache, + }, + }); + + return pool; +} + +/** Terminate worker pool and restore main-thread zarr.get chunk decode. */ +export function disableWorkerChunkDecode() { + if (activePool) { + activePool.terminateWorkers(); + activePool = undefined; + } + setChunkDecodeBackend({ kind: 'main' }); +} + +export type { GetWorkerOptions }; diff --git a/packages/zarrextra/tests/chunkDecode.spec.ts b/packages/zarrextra/tests/chunkDecode.spec.ts new file mode 100644 index 00000000..0518b661 --- /dev/null +++ b/packages/zarrextra/tests/chunkDecode.spec.ts @@ -0,0 +1,76 @@ +import * as zarr from 'zarrita'; +import { describe, expect, it, vi } from 'vitest'; +import { + getChunkDecodeBackend, + getZarrChunk, + setChunkDecodeBackend, + setFizarritaGetWorker, +} from '../src/chunkDecode'; + +const encoder = new TextEncoder(); + +function createArrayStore(): Map { + return new Map([ + [ + '/zarr.json', + encoder.encode( + JSON.stringify({ + zarr_format: 3, + node_type: 'array', + shape: [2, 2], + data_type: 'uint8', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [2, 2] }, + }, + chunk_key_encoding: { + name: 'default', + configuration: { separator: '/' }, + }, + fill_value: 0, + codecs: [{ name: 'bytes', configuration: { endian: 'little' } }], + attributes: {}, + }) + ), + ], + ['/c/0/0', new Uint8Array([1, 2, 3, 4])], + ]); +} + +describe('getZarrChunk', () => { + it('uses main-thread zarr.get by default', async () => { + setChunkDecodeBackend({ kind: 'main' }); + const arr = await zarr.open(createArrayStore() as zarr.Readable, { kind: 'array' }); + const chunk = await getZarrChunk(arr, [null, null]); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([1, 2, 3, 4]); + }); + + it('delegates to fizarrita getWorker when that backend is enabled', async () => { + const getWorker = vi.fn(async () => ({ + data: new Uint8Array([9, 8, 7, 6]), + shape: [2, 2], + stride: [2, 1], + })); + setFizarritaGetWorker(getWorker); + + const pool = { terminateWorkers: vi.fn() }; + setChunkDecodeBackend({ + kind: 'fizarrita', + pool: pool as never, + options: { workerUrl: new URL('https://example.test/codec-worker.js') }, + }); + + const arr = await zarr.open(createArrayStore() as zarr.Readable, { kind: 'array' }); + const chunk = await getZarrChunk(arr, [null, null]); + + expect(getWorker).toHaveBeenCalledOnce(); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([9, 8, 7, 6]); + + setChunkDecodeBackend({ kind: 'main' }); + }); + + it('reports the active backend', () => { + setChunkDecodeBackend({ kind: 'main' }); + expect(getChunkDecodeBackend()).toEqual({ kind: 'main' }); + }); +}); diff --git a/packages/zarrextra/tests/codecs.spec.ts b/packages/zarrextra/tests/codecs.spec.ts new file mode 100644 index 00000000..66e7328d --- /dev/null +++ b/packages/zarrextra/tests/codecs.spec.ts @@ -0,0 +1,295 @@ +import { describe, expect, it } from 'vitest'; +import * as zarr from 'zarrita'; +import { + registerExperimentalHtj2kCodec, + registerJpeg2kCodec, + wrapZarrRegistryForFizarritaWorker, +} from '../src/codecs'; + +const encoder = new TextEncoder(); + +function createCodecArrayStore(codecName: string): Map { + return new Map([ + [ + '/zarr.json', + encoder.encode( + JSON.stringify({ + zarr_format: 3, + node_type: 'array', + shape: [2, 2], + data_type: 'uint8', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [2, 2] }, + }, + chunk_key_encoding: { + name: 'default', + configuration: { separator: '/' }, + }, + fill_value: 0, + codecs: [{ name: codecName, configuration: {} }], + attributes: {}, + }) + ), + ], + ['/c/0/0', new Uint8Array([99])], + ]); +} + +describe('codec registration', () => { + it('registers JPEG2K-compatible decoders in Zarrita', async () => { + const codecName = 'imagecodecs_jpeg2k'; + const previous = zarr.registry.get(codecName); + zarr.registry.delete(codecName); + + try { + const arrBefore = await zarr.open(createCodecArrayStore(codecName) as zarr.Readable, { + kind: 'array', + }); + await expect(zarr.get(arrBefore, [null, null])).rejects.toThrow(/Unknown codec/); + + registerJpeg2kCodec({ + ids: [codecName], + decoder: () => new Uint8Array([1, 2, 3, 4]), + }); + + const arrAfter = await zarr.open(createCodecArrayStore(codecName) as zarr.Readable, { + kind: 'array', + }); + const chunk = await zarr.get(arrAfter, [null, null]); + + expect(typeof chunk).toBe('object'); + expect((chunk as zarr.Chunk<'uint8'>).shape).toEqual([2, 2]); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([1, 2, 3, 4]); + } finally { + if (previous) { + zarr.registry.set(codecName, previous); + } else { + zarr.registry.delete(codecName); + } + } + }); + + it('accepts fizarrita worker chunk metadata shape (data_type, chunk_shape)', async () => { + const codecName = 'imagecodecs_jpeg2k'; + const previous = zarr.registry.get(codecName); + zarr.registry.delete(codecName); + + try { + registerJpeg2kCodec({ + ids: [codecName], + decoder: () => new Uint8Array([5, 6, 7, 8]), + }); + + const factory = zarr.registry.get(codecName); + expect(factory).toBeDefined(); + if (!factory) throw new Error('Expected codec factory to be registered.'); + + const entry = await factory(); + const codec = entry.fromConfig({}, { + data_type: 'uint8', + chunk_shape: [2, 2], + codecs: [{ name: codecName, configuration: {} }], + }); + + const chunk = await codec.decode(new Uint8Array([99])); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([5, 6, 7, 8]); + expect((chunk as zarr.Chunk<'uint8'>).shape).toEqual([2, 2]); + } finally { + if (previous) { + zarr.registry.set(codecName, previous); + } else { + zarr.registry.delete(codecName); + } + } + }); + + it('registers OpenJPH HTJ2K decoders in Zarrita', async () => { + const codecName = 'experimental.openjph_htj2k'; + const previous = zarr.registry.get(codecName); + zarr.registry.delete(codecName); + + try { + const arrBefore = await zarr.open(createCodecArrayStore(codecName) as zarr.Readable, { + kind: 'array', + }); + await expect(zarr.get(arrBefore, [null, null])).rejects.toThrow(/Unknown codec/); + + registerExperimentalHtj2kCodec({ + ids: [codecName], + decoder: () => new Uint8Array([9, 10, 11, 12]), + }); + + const arrAfter = await zarr.open(createCodecArrayStore(codecName) as zarr.Readable, { + kind: 'array', + }); + const chunk = await zarr.get(arrAfter, [null, null]); + + expect(typeof chunk).toBe('object'); + expect((chunk as zarr.Chunk<'uint8'>).shape).toEqual([2, 2]); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([9, 10, 11, 12]); + } finally { + if (previous) { + zarr.registry.set(codecName, previous); + } else { + zarr.registry.delete(codecName); + } + } + }); + + it('still decodes legacy experimental.imagecodecs_htj2k ids', async () => { + const codecName = 'experimental.imagecodecs_htj2k'; + const previous = zarr.registry.get(codecName); + zarr.registry.delete(codecName); + + try { + registerExperimentalHtj2kCodec({ + ids: [codecName], + decoder: () => new Uint8Array([13, 14, 15, 16]), + }); + + const factory = zarr.registry.get(codecName); + expect(factory).toBeDefined(); + if (!factory) throw new Error('Expected codec factory to be registered.'); + + const entry = await factory(); + const codec = entry.fromConfig({}, { + data_type: 'uint8', + chunk_shape: [2, 2], + codecs: [{ name: codecName, configuration: {} }], + }); + + const chunk = await codec.decode(new Uint8Array([99])); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([13, 14, 15, 16]); + expect((chunk as zarr.Chunk<'uint8'>).shape).toEqual([2, 2]); + } finally { + if (previous) { + zarr.registry.set(codecName, previous); + } else { + zarr.registry.delete(codecName); + } + } + }); + + it('wrapZarrRegistryForFizarritaWorker adapts built-in codecs to fizarrita metadata', async () => { + const previousEntries = new Map(zarr.registry.entries()); + try { + wrapZarrRegistryForFizarritaWorker(); + const factory = zarr.registry.get('bytes'); + expect(factory).toBeDefined(); + if (!factory) throw new Error('Expected bytes codec factory to be registered.'); + + const entry = await factory(); + const codec = entry.fromConfig( + { endian: 'little' }, + { + data_type: 'uint8', + chunk_shape: [2, 2], + codecs: [{ name: 'bytes', configuration: { endian: 'little' } }], + } + ); + + const chunk = await codec.decode(new Uint8Array([1, 2, 3, 4])); + expect(Array.from((chunk as zarr.Chunk<'uint8'>).data)).toEqual([1, 2, 3, 4]); + expect((chunk as zarr.Chunk<'uint8'>).shape).toEqual([2, 2]); + } finally { + zarr.registry.clear(); + for (const [key, value] of previousEntries) { + zarr.registry.set(key, value); + } + } + }); + + it('encodes and decodes a small HTJ2K plane with OpenJPH WASM', async () => { + let openjph: Record; + try { + openjph = await import('@cornerstonejs/codec-openjph'); + } catch { + console.warn( + 'Skipping HTJ2K encode round-trip: @cornerstonejs/codec-openjph is not installed.' + ); + return; + } + + const { createOpenJphEncoder } = await import('../src/htj2k-encode'); + const { createOpenJphDecoder } = await import('../src/codecs'); + const factory = (openjph.default ?? openjph.OpenJPHJS ?? openjph) as Parameters< + typeof createOpenJphEncoder + >[0]; + const width = 64; + const height = 64; + const plane = new Uint16Array(width * height); + for (let y = 0; y < height; y += 1) { + for (let x = 0; x < width; x += 1) { + plane[y * width + x] = (x * 17 + y * 31) % 4096; + } + } + + const encoder = createOpenJphEncoder(factory); + const encoded = await encoder(plane, { width, height }, { reversible: true, quality: 0 }); + expect(encoded.byteLength).toBeGreaterThan(0); + + const decoder = createOpenJphDecoder(factory); + const decoded = toUint16Array(await decoder(encoded, { + dataType: 'uint16', + shape: [height, width], + codecs: [{ name: 'experimental.openjph_htj2k', configuration: {} }], + fillValue: 0, + })); + expect(decoded).toEqual(plane); + }); + + it('lossy OpenJPH quality changes encoded size on a fractal plane', async () => { + let openjph: Record; + try { + openjph = await import('@cornerstonejs/codec-openjph'); + } catch { + console.warn( + 'Skipping HTJ2K lossy quality test: @cornerstonejs/codec-openjph is not installed.' + ); + return; + } + + const { createOpenJphEncoder } = await import('../src/htj2k-encode'); + const factory = (openjph.default ?? openjph.OpenJPHJS ?? openjph) as Parameters< + typeof createOpenJphEncoder + >[0]; + const width = 64; + const height = 64; + const plane = new Uint16Array(width * height); + for (let y = 0; y < height; y += 1) { + for (let x = 0; x < width; x += 1) { + const cr = (x / width) * 3.5 - 2.5; + const ci = (y / height) * 2.0 - 1.0; + let zr = 0; + let zi = 0; + let iteration = 0; + while (zr * zr + zi * zi <= 4 && iteration < 255) { + const nr = zr * zr - zi * zi + cr; + zi = 2 * zr * zi + ci; + zr = nr; + iteration += 1; + } + plane[y * width + x] = (iteration * 16) % 4096; + } + } + + const encoder = createOpenJphEncoder(factory); + const high = await encoder(plane, { width, height }, { reversible: false, quality: 0.001 }); + const mid = await encoder(plane, { width, height }, { reversible: false, quality: 0.01 }); + const low = await encoder(plane, { width, height }, { reversible: false, quality: 0.1 }); + + expect(high.byteLength).toBeGreaterThan(mid.byteLength); + expect(mid.byteLength).toBeGreaterThan(low.byteLength); + }); +}); + +function toUint16Array(data: ArrayBuffer | ArrayBufferView): Uint16Array { + if (data instanceof Uint16Array) { + return data; + } + if (ArrayBuffer.isView(data)) { + return new Uint16Array(data.buffer, data.byteOffset, data.byteLength / 2); + } + return new Uint16Array(data); +} diff --git a/packages/zarrextra/tests/omeZarr.spec.ts b/packages/zarrextra/tests/omeZarr.spec.ts new file mode 100644 index 00000000..892456ae --- /dev/null +++ b/packages/zarrextra/tests/omeZarr.spec.ts @@ -0,0 +1,215 @@ +import { describe, expect, it } from 'vitest'; +import * as zarr from 'zarrita'; +import { loadOmeZarrMultiscalesFromStore, registerJpeg2kCodec } from '../src'; + +const encoder = new TextEncoder(); + +function jsonBytes(value: unknown): Uint8Array { + return encoder.encode(JSON.stringify(value)); +} + +type OmeAxisSpec = { name: string; type?: string; unit?: string }; + +function createRawArrayMetadata(shape: number[], chunkShape: number[]) { + return { + zarr_format: 3, + node_type: 'array', + shape, + data_type: 'uint8', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: chunkShape }, + }, + chunk_key_encoding: { + name: 'default', + configuration: { separator: '/' }, + }, + fill_value: 0, + codecs: [{ name: 'bytes', configuration: { endian: 'little' } }], + attributes: {}, + }; +} + +function createOmeZarrGroupStore( + axes: OmeAxisSpec[], + arrayMetadata: Record, + chunks: Map +): Map { + const store = new Map([ + [ + '/zarr.json', + jsonBytes({ + zarr_format: 3, + node_type: 'group', + attributes: { + ome: { + multiscales: [ + { + axes, + datasets: [{ path: '0' }], + }, + ], + }, + }, + consolidated_metadata: { + kind: 'inline', + must_understand: false, + metadata: { + '0': arrayMetadata, + }, + }, + }), + ], + ]); + for (const [path, bytes] of chunks) { + store.set(path, bytes); + } + return store; +} + +function createOmeZarrStore(): Map { + return createOmeZarrGroupStore( + [ + { name: 't', type: 'time' }, + { name: 'c', type: 'channel' }, + { name: 'z', type: 'space' }, + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + { + ...createRawArrayMetadata([1, 1, 1, 2, 2], [1, 1, 1, 2, 2]), + codecs: [{ name: 'imagecodecs_jpeg2k', configuration: {} }], + }, + new Map([['/0/c/0/0/0/0/0', new Uint8Array([99])]]) + ); +} + +function indexedVolumeValue(t: number, c: number, z: number, y: number, x: number): number { + return t * 100 + c * 10 + z + y * 4 + x; +} + +function createMultiTzOmeZarrStore(): Map { + const shape = [2, 1, 3, 4, 4]; + const chunkShape = [1, 1, 1, 4, 4]; + const chunks = new Map(); + + for (let t = 0; t < shape[0]; t += 1) { + for (let z = 0; z < shape[2]; z += 1) { + const plane = new Uint8Array(shape[3] * shape[4]); + for (let y = 0; y < shape[3]; y += 1) { + for (let x = 0; x < shape[4]; x += 1) { + plane[y * shape[4] + x] = indexedVolumeValue(t, 0, z, y, x); + } + } + chunks.set(`/0/c/${t}/0/${z}/0/0`, plane); + } + } + + return createOmeZarrGroupStore( + [ + { name: 't', type: 'time' }, + { name: 'c', type: 'channel' }, + { name: 'z', type: 'space' }, + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + createRawArrayMetadata(shape, chunkShape), + chunks + ); +} + +function createZcyxOmeZarrStore(): Map { + const shape = [3, 2, 8, 8]; + const chunkShape = [1, 1, 8, 8]; + const plane = new Uint8Array(8 * 8); + for (let y = 0; y < 8; y += 1) { + for (let x = 0; x < 8; x += 1) { + plane[y * 8 + x] = y * 8 + x; + } + } + + const chunks = new Map(); + for (let z = 0; z < shape[0]; z += 1) { + for (let c = 0; c < shape[1]; c += 1) { + chunks.set(`/0/c/${z}/${c}/0/0`, plane); + } + } + + return createOmeZarrGroupStore( + [ + { name: 'z', type: 'space' }, + { name: 'c', type: 'channel' }, + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + createRawArrayMetadata(shape, chunkShape), + chunks + ); +} + +describe('OME-Zarr store loader', () => { + it('creates Viv-compatible PixelSources backed by workspace Zarrita', async () => { + const previous = zarr.registry.get('imagecodecs_jpeg2k'); + registerJpeg2kCodec({ + ids: ['imagecodecs_jpeg2k'], + decoder: () => new Uint8Array([1, 2, 3, 4]), + }); + + try { + const [source] = await loadOmeZarrMultiscalesFromStore(createOmeZarrStore() as zarr.Readable); + expect(source.labels).toEqual(['t', 'c', 'z', 'y', 'x']); + expect(source.shape).toEqual([1, 1, 1, 2, 2]); + expect(source.dtype).toBe('Uint8'); + + const tile = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + expect(tile.width).toBe(2); + expect(tile.height).toBe(2); + expect(Array.from(tile.data as Uint8Array)).toEqual([1, 2, 3, 4]); + } finally { + if (previous) { + zarr.registry.set('imagecodecs_jpeg2k', previous); + } else { + zarr.registry.delete('imagecodecs_jpeg2k'); + } + } + }); + + it('returns distinct tiles for different z and t selections', async () => { + const [source] = await loadOmeZarrMultiscalesFromStore( + createMultiTzOmeZarrStore() as zarr.Readable + ); + expect(source.shape).toEqual([2, 1, 3, 4, 4]); + + const tileTz0 = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + const tileTz1 = await source.getTile({ x: 0, y: 0, selection: { t: 1, c: 0, z: 2 } }); + + expect(tileTz0.width).toBe(4); + expect(tileTz0.height).toBe(4); + expect((tileTz0.data as Uint8Array)[0]).toBe(indexedVolumeValue(0, 0, 0, 0, 0)); + expect((tileTz1.data as Uint8Array)[0]).toBe(indexedVolumeValue(1, 0, 2, 0, 0)); + expect((tileTz0.data as Uint8Array)[0]).not.toBe((tileTz1.data as Uint8Array)[0]); + }); + + it('defaults missing z/t selection axes to index 0', async () => { + const [source] = await loadOmeZarrMultiscalesFromStore( + createMultiTzOmeZarrStore() as zarr.Readable + ); + + const explicit = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + const defaulted = await source.getTile({ x: 0, y: 0, selection: { c: 0 } }); + + expect((defaulted.data as Uint8Array)[0]).toBe((explicit.data as Uint8Array)[0]); + }); + + it('resolves spatial axes from labels for non-canonical axis order', async () => { + const [source] = await loadOmeZarrMultiscalesFromStore(createZcyxOmeZarrStore() as zarr.Readable); + expect(source.labels).toEqual(['z', 'c', 'y', 'x']); + expect(source.shape).toEqual([3, 2, 8, 8]); + + const tile = await source.getTile({ x: 0, y: 0, selection: { z: 1, c: 0 } }); + expect(tile.width).toBe(8); + expect(tile.height).toBe(8); + expect((tile.data as Uint8Array)[0]).toBe(0); + expect((tile.data as Uint8Array)[7]).toBe(7); + }); +}); diff --git a/packages/zarrextra/tests/workers.spec.ts b/packages/zarrextra/tests/workers.spec.ts new file mode 100644 index 00000000..26d62092 --- /dev/null +++ b/packages/zarrextra/tests/workers.spec.ts @@ -0,0 +1,33 @@ +import { afterEach, describe, expect, it, vi } from 'vitest'; +import { getChunkDecodeBackend } from '../src/chunkDecode'; +import { disableWorkerChunkDecode, enableWorkerChunkDecode } from '../src/workers/index'; + +vi.mock('@fideus-labs/worker-pool', () => { + class MockWorkerPool { + terminateWorkers = vi.fn(); + } + return { WorkerPool: MockWorkerPool }; +}); + +describe('worker chunk decode setup', () => { + afterEach(() => { + disableWorkerChunkDecode(); + }); + + it('enables the fizarrita chunk decode backend', () => { + enableWorkerChunkDecode({ workers: 2 }); + expect(getChunkDecodeBackend()).toMatchObject({ + kind: 'fizarrita', + options: { + workerUrl: expect.any(URL), + }, + }); + }); + + it('resets to main-thread decode on disable', () => { + const pool = enableWorkerChunkDecode({ workers: 2 }); + disableWorkerChunkDecode(); + expect(getChunkDecodeBackend()).toEqual({ kind: 'main' }); + expect(pool.terminateWorkers).toHaveBeenCalledOnce(); + }); +}); diff --git a/packages/zarrextra/vite.config.ts b/packages/zarrextra/vite.config.ts index 90aa7dd6..3597ca50 100644 --- a/packages/zarrextra/vite.config.ts +++ b/packages/zarrextra/vite.config.ts @@ -2,26 +2,41 @@ import { resolve } from 'node:path'; import { defineConfig } from 'vitest/config'; import dts from 'vite-plugin-dts'; +const pkgExternals = ['zarrita', '@fideus-labs/fizarrita', '@fideus-labs/worker-pool']; + export default defineConfig({ plugins: [ dts({ outDir: 'dist', include: ['src'], - exclude: ['**/*.test.ts'], + exclude: ['**/*.test.ts', 'src/workers/codec-worker.ts'], }), ], build: { lib: { - entry: resolve(__dirname, 'src/index.ts'), - name: 'Zarrextra', - formats: ['es', 'cjs'], - fileName: (format) => `index.${format === 'es' ? 'js' : 'cjs'}`, + entry: { + index: resolve(__dirname, 'src/index.ts'), + workers: resolve(__dirname, 'src/workers/index.ts'), + 'codec-worker': resolve(__dirname, 'src/workers/codec-worker.ts'), + }, + formats: ['es'], }, rollupOptions: { - external: ['zarrita'], + external(id, parentId) { + if (parentId?.includes('codec-worker')) { + return false; + } + if (parentId?.includes('workers')) { + return pkgExternals.includes(id); + } + return id === 'zarrita'; + }, + output: { + entryFileNames: '[name].js', + }, }, sourcemap: true, - target: 'es2020', + target: 'es2022', }, test: { globals: true, diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 209c1192..784796f6 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -174,6 +174,9 @@ importers: react-dom: specifier: '>=18 <20' version: 19.2.1(react@19.2.1) + zarrextra: + specifier: workspace:* + version: link:../zarrextra zustand: specifier: ^5.0.8 version: 5.0.8(@types/react@19.2.2)(react@19.2.1)(use-sync-external-store@1.6.0(react@19.2.1)) @@ -342,7 +345,7 @@ importers: version: 9.2.11 '@hms-dbmi/viv': specifier: 'catalog:' - version: 0.21.0(682892a736d1d10c2d929b2464c0e937) + version: 0.21.0(34b22613fa33583b145acc9b31a1f375) '@luma.gl/core': specifier: 'catalog:' version: 9.2.6 @@ -363,10 +366,10 @@ importers: version: link:../react '@uidotdev/usehooks': specifier: ^2.4.1 - version: 2.4.1(react-dom@19.2.0(react@19.2.0))(react@19.2.0) + version: 2.4.1(react-dom@19.2.1(react@19.2.1))(react@19.2.1) '@uiw/react-json-view': specifier: 2.0.0-alpha.39 - version: 2.0.0-alpha.39(@babel/runtime@7.28.4)(react-dom@19.2.0(react@19.2.0))(react@19.2.0) + version: 2.0.0-alpha.39(@babel/runtime@7.28.4)(react-dom@19.2.1(react@19.2.1))(react@19.2.1) '@vivjs/views': specifier: 'catalog:' version: 0.21.0(f5ace54b53b72239a461a3179859574d) @@ -375,7 +378,7 @@ importers: version: 0.0.2 deck.gl: specifier: 'catalog:' - version: 9.2.11(@arcgis/core@4.34.5)(@luma.gl/constants@9.2.6)(@luma.gl/gltf@9.2.6(@luma.gl/constants@9.2.6)(@luma.gl/core@9.2.6)(@luma.gl/engine@9.2.6(@luma.gl/core@9.2.6)(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6)))(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6)))(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6))(@luma.gl/webgl@9.2.6(@luma.gl/core@9.2.6))(@math.gl/web-mercator@4.1.0)(react-dom@19.2.0(react@19.2.0))(react@19.2.0) + version: 9.2.11(@arcgis/core@4.34.5)(@luma.gl/constants@9.2.6)(@luma.gl/gltf@9.2.6(@luma.gl/constants@9.2.6)(@luma.gl/core@9.2.6)(@luma.gl/engine@9.2.6(@luma.gl/core@9.2.6)(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6)))(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6)))(@luma.gl/shadertools@9.2.6(@luma.gl/core@9.2.6))(@luma.gl/webgl@9.2.6(@luma.gl/core@9.2.6))(@math.gl/web-mercator@4.1.0)(react-dom@19.2.1(react@19.2.1))(react@19.2.1) fast-deep-equal: specifier: ^3.1.3 version: 3.1.3 @@ -384,17 +387,23 @@ importers: version: 2.1.4-beta.0 react: specifier: '>=18 <20' - version: 19.2.0 + version: 19.2.1 react-dom: specifier: '>=18 <20' - version: 19.2.0(react@19.2.0) + version: 19.2.1(react@19.2.1) zarrita: specifier: 'catalog:' version: 0.7.1 zustand: specifier: ^5.0.8 - version: 5.0.8(@types/react@19.2.2)(react@19.2.0)(use-sync-external-store@1.6.0(react@19.2.0)) + version: 5.0.8(@types/react@19.2.2)(react@19.2.1)(use-sync-external-store@1.6.0(react@19.2.1)) devDependencies: + '@cornerstonejs/codec-openjpeg': + specifier: ^1.3.0 + version: 1.3.0 + '@cornerstonejs/codec-openjph': + specifier: ^2.4.7 + version: 2.4.7 '@types/node': specifier: 'catalog:' version: 22.18.8 @@ -447,6 +456,19 @@ importers: vitest: specifier: 'catalog:' version: 4.1.4(@opentelemetry/api@1.9.0)(@types/node@22.18.8)(jsdom@27.4.0)(vite@8.0.8(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) + optionalDependencies: + '@cornerstonejs/codec-openjpeg': + specifier: ^1.3.0 + version: 1.3.0 + '@cornerstonejs/codec-openjph': + specifier: ^2.4.7 + version: 2.4.7 + '@fideus-labs/fizarrita': + specifier: ^1.4.1 + version: 1.4.1(zarrita@0.7.1) + '@fideus-labs/worker-pool': + specifier: ^1.0.0 + version: 1.0.0 packages: @@ -1274,6 +1296,14 @@ packages: resolution: {integrity: sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==} engines: {node: '>=0.1.90'} + '@cornerstonejs/codec-openjpeg@1.3.0': + resolution: {integrity: sha512-hP8WAZ63AcaDYmHbBVTY04x424AglXsRHrI6VBdW4eTiJ76f0heWrEodT9Sb3sNwazzYuyMOIZNndJPeVSeHcw==} + engines: {node: '>=0.14'} + + '@cornerstonejs/codec-openjph@2.4.7': + resolution: {integrity: sha512-qvP4q4JDib7mi9r7LqKOwqz7YZ8gjtDX4ZCezeYf8+eb7MBXCz5uXAMeVF3yz9Axw4XiIMdB/pqXkm8tqCl13w==} + engines: {node: '>=0.14'} + '@csstools/cascade-layer-name-parser@2.0.5': resolution: {integrity: sha512-p1ko5eHgV+MgXFVa4STPKpvPxr6ReS8oS2jzTukjR74i5zJNyWO1ZM1m8YKBXnzDKWfBN1ztLYlHxbVemDD88A==} engines: {node: '>=18'} @@ -1877,6 +1907,14 @@ packages: '@noble/hashes': optional: true + '@fideus-labs/fizarrita@1.4.1': + resolution: {integrity: sha512-71HTW4cTDeUnm2f3MU3352MMlpzUAFHhDmEajaASpUywVDe7RdY8ImjeXwRllKjvfPcukfz/aEmdPs67esSngA==} + peerDependencies: + zarrita: '>=0.6.0' + + '@fideus-labs/worker-pool@1.0.0': + resolution: {integrity: sha512-Mwx8fFKKpTUcEtR7w45MQJ/RnZFUPBtefEvGTZGlZMAVSfD7W61rpB8ZdgS4V0CXfppwcb90BF7F/aANWvupnA==} + '@floating-ui/core@1.7.3': resolution: {integrity: sha512-sGnvb5dmrJaKEZ+LDIpguvdX3bDlEllmv4/ClQ9awcmCZrlx5jQyyMWFM5kBI+EyNOCDDiKk8il0zeuX3Zlg/w==} @@ -9042,6 +9080,10 @@ snapshots: '@colors/colors@1.5.0': optional: true + '@cornerstonejs/codec-openjpeg@1.3.0': {} + + '@cornerstonejs/codec-openjph@2.4.7': {} + '@csstools/cascade-layer-name-parser@2.0.5(@csstools/css-parser-algorithms@3.0.5(@csstools/css-tokenizer@3.0.4))(@csstools/css-tokenizer@3.0.4)': dependencies: '@csstools/css-parser-algorithms': 3.0.5(@csstools/css-tokenizer@3.0.4) @@ -9492,13 +9534,6 @@ snapshots: transitivePeerDependencies: - '@loaders.gl/core' - '@deck.gl/react@9.2.11(@deck.gl/core@9.2.11)(@deck.gl/widgets@9.2.11(@deck.gl/core@9.2.11)(@luma.gl/core@9.2.6))(react-dom@19.2.0(react@19.2.0))(react@19.2.0)': - dependencies: - '@deck.gl/core': 9.2.11 - '@deck.gl/widgets': 9.2.11(@deck.gl/core@9.2.11)(@luma.gl/core@9.2.6) - react: 19.2.0 - react-dom: 19.2.0(react@19.2.0) - '@deck.gl/react@9.2.11(@deck.gl/core@9.2.11)(@deck.gl/widgets@9.2.11(@deck.gl/core@9.2.11)(@luma.gl/core@9.2.6))(react-dom@19.2.1(react@19.2.1))(react@19.2.1)': dependencies: '@deck.gl/core': 9.2.11 @@ -10328,6 +10363,15 @@ snapshots: '@exodus/bytes@1.10.0': {} + '@fideus-labs/fizarrita@1.4.1(zarrita@0.7.1)': + dependencies: + '@fideus-labs/worker-pool': 1.0.0 + zarrita: 0.7.1 + optional: true + + '@fideus-labs/worker-pool@1.0.0': + optional: true + '@floating-ui/core@1.7.3': dependencies: '@floating-ui/utils': 0.2.10 @@ -10392,27 +10436,6 @@ snapshots: - '@luma.gl/webgl' - react - '@hms-dbmi/viv@0.21.0(682892a736d1d10c2d929b2464c0e937)': - dependencies: - 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use-sync-external-store@1.6.0(react@19.2.0): - dependencies: - react: 19.2.0 - optional: true - use-sync-external-store@1.6.0(react@19.2.1): dependencies: react: 19.2.1 @@ -17199,12 +17169,6 @@ snapshots: zstddec@0.2.0-alpha.3: {} - zustand@5.0.8(@types/react@19.2.2)(react@19.2.0)(use-sync-external-store@1.6.0(react@19.2.0)): - optionalDependencies: - '@types/react': 19.2.2 - react: 19.2.0 - use-sync-external-store: 1.6.0(react@19.2.0) - zustand@5.0.8(@types/react@19.2.2)(react@19.2.1)(use-sync-external-store@1.6.0(react@19.2.1)): optionalDependencies: '@types/react': 19.2.2 diff --git a/python/spatialdata-codec-writer/README.md b/python/spatialdata-codec-writer/README.md new file mode 100644 index 00000000..19a3016b --- /dev/null +++ b/python/spatialdata-codec-writer/README.md @@ -0,0 +1,218 @@ +# spatialdata-codec-writer + +Publishable Python tool for recompressing SpatialData/OME-Zarr image stores with +optional browser-targeted codecs (JPEG 2000 and experimental HTJ2K, which is computationally cheaper). + +This is a working prototype that may be used for experimenting with writing non-standard +stores that can as of this writing only be interpreted by the `spatialdata.js` runtime. +It is hoped that if found to be of benefit, these codecs can be adopted more broadly. +We may also review other options for comparison. + +The package vendors OpenJPH WASM and runs it through a pool of persistent Node.js +encoder workers. **Runtime requirements:** Python 3.12+, Node.js on PATH, and +`imagecodecs` for JP2K encode/decode validation. + +Codec test fixture generation lives in this repository under +`python/spatialdata-codec-writer/scripts/` (not exported from the installed wheel). + +## Install + +```bash +pip install spatialdata-codec-writer +``` + +For local development in this monorepo: + +```bash +pnpm test:codec-writer +``` + +(`openjphjs.js` / `openjphjs.wasm` are gitignored; the script vendors them from +`@cornerstonejs/codec-openjph` before pytest.) + +Before building or running HTJ2K tests manually: + +```bash +node scripts/vendor-openjph-for-python.mjs +uv run --directory python/spatialdata-codec-writer pytest +``` + +## Recompress an existing SpatialData store + +Use `recompress_spatialdata` or the `recompress` CLI when you want to preserve a +whole SpatialData object and rewrite selected raster payloads. Path sources are +copied first, so tables, shapes, points, root `spatialdata_attrs`, and +unconfigured rasters are preserved without loading the full object. + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress input.sdata.zarr output-jp2k.zarr --image-key morphology_focus --preset balanced --chunks auto --overwrite +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress input.sdata.zarr output-htj2k.zarr --image-key morphology_focus --codec experimental.openjph_htj2k --preset balanced --chunks auto --overwrite +``` + +To recompress **every** image with the same settings, omit `--image-key`; CLI flags update +`default_image` and apply to all image groups in the store: + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress \ + input.sdata.zarr output-htj2k.zarr \ + --codec experimental.openjph_htj2k \ + --quality 0.0005 \ + --chunks auto \ + --sibling \ + --overwrite +``` + +With `--sibling`, each original image is kept and a compressed sibling is added alongside it +(e.g. `morphology_focus:htj2k_q0.0005`, `he_image:htj2k_q0.0005`). + +Parallel encoding defaults to one worker per CPU (`--workers N` to override). + +### Custom HTJ2K `quality` (instead of `--preset`) + +Presets are shortcuts. For per-dataset tuning, pass an explicit OpenJPH quantization +factor. **Lower `quality` = higher fidelity and larger output** (not JP2K-style 0–100). + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress \ + input.sdata.zarr output-htj2k.zarr \ + --image-key morphology_focus \ + --codec experimental.openjph_htj2k \ + --quality 0.001 \ + --chunks auto \ + --sibling \ + --overwrite +``` + +With `--sibling`, the new image is named from the quality, e.g. +`morphology_focus:htj2k_q0.001`. + +Equivalent JSON config: + +```json +{ + "images": { + "morphology_focus": { + "codec": "experimental.openjph_htj2k", + "quality": 0.001, + "chunks": "auto" + } + } +} +``` + +For repeatable runs with multiple images, prefer a JSON config file: + +```json +{ + "default_image": { "codec": "imagecodecs_jpeg2k", "preset": "lossless", "chunks": "auto" }, + "images": { + "morphology_focus": { "preset": "balanced" }, + "he_image": { "preset": "small" }, + "fast_preview": { + "codec": "experimental.openjph_htj2k", + "preset": "lossless", + "chunks": "auto" + } + }, + "default_labels": { "codec": "blosc", "clevel": 5 } +} +``` + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer recompress input.sdata.zarr output-jp2k.zarr --config recompress.json --overwrite +``` + +JP2K presets: + +- `lossless`: reversible JP2K with exact round-trip validation. +- `balanced`: near-lossless JP2K (`level=100`). +- `small`: more compact JP2K (`level=75`). + +HTJ2K encode uses vendored OpenJPH WASM (`experimental.openjph_htj2k`, +`encoder: openjph-wasm` in manifests). Presets call +`HTJ2KEncoder.setQuality(reversible, quality)`: + +- `lossless`: `reversible=True`. +- `balanced`: `reversible=False`, `quality=0.0002`. +- `small`: `reversible=False`, `quality=0.001`. + +See [`docs/htj2k-wasm-encode-design.md`](docs/htj2k-wasm-encode-design.md) for +calibration notes. + +Labels are written with Blosc/zstd by default. Browser-targeted image codecs +support `uint8`, `int8`, `uint16`, and `int16` only. + +The recompressor writes a sidecar manifest beside the output with the expanded +config, per-raster metadata, encoded byte counts, package versions, and +representative decoded checksums. Tool provenance lives in the manifest; source +store root `spatialdata_attrs` are preserved from the copy. + +## Inspect manifests + +```bash +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer inspect output-jp2k.manifest.json +``` + +## Generate codec fixtures (monorepo dev only) + +Fixture generation is **not** part of the published CLI. From the repository root: + +```bash +pnpm test:fixtures:generate:codecs +``` + +Or directly: + +```bash +node scripts/vendor-openjph-for-python.mjs +uv run --directory python/spatialdata-codec-writer python scripts/generate_codec_fixtures.py --output-dir ../../test-fixtures/codecs --experimental-htj2k --overwrite +``` + +Dev fixtures stamp root metadata with `experimental_codec_writer` (not a fake +`spatialdata` library version) to signal they are codec test artifacts. See +`docs/docs/vis/codec-fixtures.mdx` for browser demo instructions and a note on +provenance standardization. + +### Manual multi-dimensional volumes + +Default generated fixtures use shape `[1, 1, 1, H, W]`. For ad-hoc synthetic stores, use +`write-synthetic`: + +```bash +# From the monorepo root (pnpm forwards extra args after --) +pnpm write-synthetic -- ~/data/spatialdata/sdata_inputs/mandelbulb.zarr \ + --pattern mandelbulb --size 1024 --z 128 --t 1 --c 1 \ + --image-key mandelbulb --chunk-spatial 256 --overwrite + +# Or directly via uv +node scripts/vendor-openjph-for-python.mjs +uv run --directory python/spatialdata-codec-writer spatialdata-codec-writer-write-synthetic \ + ~/path/out.zarr --pattern indexed --size 64 --t 2 --z 3 --codec imagecodecs_jpeg2k +``` + +Patterns: `mandelbulb` (default), `indexed`, `mandelbrot` (single 2D plane), `fractal` +(legacy fixture shape). HTJ2K is the default codec; use `--preset balanced` or +`--quality 0.001` for lossy output. + +Richer, biologically motivated or compression-aware synthesis is planned +possibly as future JS-side tooling rather than growing this Python module further. + +## Python API + +```python +from spatialdata_codec_writer import recompress_spatialdata + +result = recompress_spatialdata( + "input.sdata.zarr", + "output-jp2k.zarr", + image_key="morphology_focus", + preset="balanced", + chunks="auto", + overwrite=True, + workers=4, +) +print(result.manifest_path) +``` + +TypeScript callers can use `encodeHtj2kPlane()` from `zarrextra` directly. +See [htj2k-wasm-encode-design.md](docs/htj2k-wasm-encode-design.md). diff --git a/python/spatialdata-codec-writer/docs/htj2k-wasm-encode-design.md b/python/spatialdata-codec-writer/docs/htj2k-wasm-encode-design.md new file mode 100644 index 00000000..a2423da1 --- /dev/null +++ b/python/spatialdata-codec-writer/docs/htj2k-wasm-encode-design.md @@ -0,0 +1,110 @@ +# HTJ2K OpenJPH WASM encode + +Status: **implemented** — HTJ2K encode uses vendored OpenJPH WASM inside a pool +of persistent Node.js workers (`spatialdata_codec_writer/vendor/encode-plane.mjs`). +New stores are labelled `experimental.openjph_htj2k`. + +Native `imagecodecs` HTJ2K encode is intentionally **not** used: PyPI wheels are +often stub-only, conda installs are awkward, and the WASM encoder exposes +`setQuality(reversible, quality)` for preset control. We may re-evaluate native +encode later; the frontend still decodes the legacy id +`experimental.imagecodecs_htj2k` for older fixtures. + +## Contracts + +| Contract | Detail | +|----------|--------| +| Zarr codec id (new writes) | `experimental.openjph_htj2k` | +| Zarr codec id (legacy decode) | `experimental.imagecodecs_htj2k` | +| Encoder label | `openjph-wasm` (manifest `encoder` field) | +| Array metadata | Zarr v3; `codecs: [{ name, configuration: {} }]` | +| Chunk bytes | Raw HTJ2K bitstream per 2D spatial plane (last two axes) | +| Browser read | `registerExperimentalHtj2kCodec()` registers both ids | + +## Encode flow + +```text +Python spatialdata-codec-writer + → EncoderPool (N persistent Node workers) + → vendored encode-plane.mjs --worker + → OpenJPH HTJ2KEncoder.setQuality(reversible, quality).encode() + → HTJ2K bytes per chunk +``` + +Vendoring: run `node scripts/vendor-openjph-for-python.mjs` at the monorepo root +to copy `@cornerstonejs/codec-openjph` dist assets into the Python package wheel. +The copied `vendor/openjph/` blobs are gitignored; CI and `pnpm test:codec-writer` +run the vendor step after `pnpm install`. + +Preset mapping: + +| Preset | `setQuality(reversible, quality)` | +|--------|-----------------------------------| +| `lossless` | `(true, 0)` | +| `balanced` | `(false, 0.0002)` | +| `small` | `(false, 0.001)` | + +`quality` is a float quantization factor (lower = better fidelity, larger output). +Integer values above ~15 with `reversible=false` produce degenerate output. + +### Preset calibration (rough) + +Early presets (`balanced: 0.005`, `small: 0.01`) were tuned on 64×64 Mandelbrot +fixtures. On full-range Xenium morphology `uint16` chunks (1024×1024 planes), that +`balanced` setting was far more lossy than JP2K `balanced` (`level=100`). + +Spot checks on one morphology pyramid chunk (`RMSE` on decoded vs source): + +| Setting | Encoded (1024² `uint16`) | RMSE | +|---------|--------------------------|------| +| JP2K `balanced` | ~722 KiB | ~0.3 | +| HTJ2K `q=0.0002` (new `balanced`) | ~419 KiB | ~5 | +| HTJ2K `q=0.001` (new `small`) | ~128 KiB | ~22 | +| HTJ2K `q=0.005` (old `balanced`) | ~39 KiB | ~60 | + +Preset names are aligned **roughly** with JP2K intent on real morphology data, +not bit-identical rate control. For per-dataset tuning, prefer explicit `quality` +rather than presets alone. + +### CLI and JSON + +```bash +spatialdata-codec-writer recompress input.zarr output.zarr \ + --image-key morphology_focus \ + --codec experimental.openjph_htj2k \ + --quality 0.001 \ + --sibling \ + --workers 4 \ + --overwrite +``` + +```json +{ + "images": { + "morphology_focus": { + "codec": "experimental.openjph_htj2k", + "quality": 0.001 + } + } +} +``` + +Setting `quality` implies `reversible=false` unless `reversible` is explicitly +`true`. Sibling outputs use `morphology_focus:htj2k_q0.001` when quality is set. + +**Future:** add browser UI on the codec demo route to interactively transcode a +region or layer at arbitrary `q` and compare size/RMSE side by side (the +`htj2k-demo.zarr` multi-layer fixture is a step toward that). + +`htj2k-quality-sweep.manifest.json` records encoded sizes and RMSE for a 64×64 +Mandelbrot plane across several qualities. + +## References + +- Python encode: [`htj2k_encode.py`](../src/spatialdata_codec_writer/htj2k_encode.py), + [`codecs.py`](../src/spatialdata_codec_writer/codecs.py) +- Vendored Node worker: [`vendor/encode-plane.mjs`](../src/spatialdata_codec_writer/vendor/encode-plane.mjs) +- Vendor script: [`scripts/vendor-openjph-for-python.mjs`](../../../scripts/vendor-openjph-for-python.mjs) +- Dev fixtures: [`scripts/generate_codec_fixtures.py`](../scripts/generate_codec_fixtures.py) +- JS encode: [`packages/zarrextra/src/htj2k-encode.ts`](../../../packages/zarrextra/src/htj2k-encode.ts) +- JS decode: [`packages/zarrextra/src/codecs.ts`](../../../packages/zarrextra/src/codecs.ts) diff --git a/python/spatialdata-codec-writer/pyproject.toml b/python/spatialdata-codec-writer/pyproject.toml new file mode 100644 index 00000000..48bead4f --- /dev/null +++ b/python/spatialdata-codec-writer/pyproject.toml @@ -0,0 +1,46 @@ +[project] +name = "spatialdata-codec-writer" +version = "0.1.0" +description = "Recompress SpatialData/OME-Zarr image stores with optional JP2K and HTJ2K codecs" +requires-python = ">=3.12" +readme = "README.md" +license = { text = "MIT" } +authors = [{ name = "SpatialData.ts contributors" }] +dependencies = [ + "dask[array]>=2025.0", + "imagecodecs>=2025.8.2", + "numcodecs>=0.16", + "numpy>=2.0", + "ome-zarr>=0.13", + "spatialdata>=0.7.2", + "zarr>=3.1", +] + +[project.scripts] +spatialdata-codec-writer = "spatialdata_codec_writer.cli:main" +spatialdata-codec-writer-write-synthetic = "spatialdata_codec_writer.synthetic_cli:main" + +[build-system] +requires = ["setuptools>=68"] +build-backend = "setuptools.build_meta" + +[tool.setuptools.packages.find] +where = ["src"] + +[tool.setuptools.package-data] +spatialdata_codec_writer = ["vendor/openjph/*", "vendor/encode-plane.mjs"] + +[tool.uv] +package = true + +[tool.pytest.ini_options] +testpaths = ["tests"] + +[tool.basedpyright] +extraPaths = ["scripts"] + +[dependency-groups] +dev = [ + "pytest>=8.0", +] + diff --git a/python/spatialdata-codec-writer/scripts/fixture_writer.py b/python/spatialdata-codec-writer/scripts/fixture_writer.py new file mode 100644 index 00000000..fb9fea28 --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/fixture_writer.py @@ -0,0 +1,483 @@ +from __future__ import annotations + +import shutil +from dataclasses import dataclass +from pathlib import Path +from typing import Any + +import numpy as np + +from spatialdata_codec_writer.codecs import ( + CODEC_HTJ2K_OPENJPH, + CODEC_JPEG2K, + HTJ2K_ENCODER, + CodecName, + chunk_grid, + decode_image_plane, + encode_image_plane, + is_htj2k_codec, + package_version, + sha256, + write_json, +) +from spatialdata_codec_writer.htj2k_encode import openjph_encode_options + +from provenance import experimental_codec_writer_attrs + + +@dataclass(frozen=True) +class WrittenFixture: + store_path: Path + manifest_path: Path + manifest: dict[str, Any] + + +@dataclass(frozen=True) +class CodecImageWrite: + image_key: str + image: Any + encode_options: dict[str, Any] | None = None + + +def _default_image() -> np.ndarray: + y, x = np.mgrid[0:64, 0:64] + image = ((x * 17 + y * 31) % 4096).astype(np.uint16) + return image.reshape(1, 1, 1, 64, 64) + + +def _downsample2(image: np.ndarray) -> np.ndarray: + return image[..., ::2, ::2].copy() + + +def _extract_chunk(image: np.ndarray, chunks: tuple[int, ...], coords: tuple[int, ...]) -> np.ndarray: + slices = [] + for coord, chunk, size in zip(coords, chunks, image.shape): + start = coord * chunk + stop = min(start + chunk, size) + slices.append(slice(start, stop)) + chunk_data = image[tuple(slices)] + if chunk_data.shape == chunks: + return chunk_data + + padded = np.zeros(chunks, dtype=image.dtype) + padded_slices = tuple(slice(0, size) for size in chunk_data.shape) + padded[padded_slices] = chunk_data + return padded + + +def _array_metadata(shape: tuple[int, ...], chunks: tuple[int, ...], dtype: np.dtype, codec: str) -> dict[str, Any]: + return { + "zarr_format": 3, + "node_type": "array", + "shape": list(shape), + "data_type": np.dtype(dtype).name, + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": list(chunks)}, + }, + "chunk_key_encoding": { + "name": "default", + "configuration": {"separator": "/"}, + }, + "fill_value": 0, + "codecs": [{"name": codec, "configuration": {}}], + "attributes": {}, + "dimension_names": ["t", "c", "z", "y", "x"], + } + + +def _group_metadata(attributes: dict[str, Any] | None = None) -> dict[str, Any]: + return { + "zarr_format": 3, + "node_type": "group", + "attributes": attributes or {}, + } + + +def _image_attrs(datasets: list[dict[str, Any]], image_key: str) -> dict[str, Any]: + return { + "ome": { + "multiscales": [ + { + "name": image_key, + "axes": [ + {"name": "t", "type": "time"}, + {"name": "c", "type": "channel"}, + {"name": "z", "type": "space", "unit": "micrometer"}, + {"name": "y", "type": "space", "unit": "micrometer"}, + {"name": "x", "type": "space", "unit": "micrometer"}, + ], + "datasets": datasets, + "coordinateTransformations": [ + { + "type": "identity", + "output": { + "name": "global", + "axes": [ + {"name": "z", "type": "space", "unit": "micrometer"}, + {"name": "y", "type": "space", "unit": "micrometer"}, + {"name": "x", "type": "space", "unit": "micrometer"}, + ], + }, + } + ], + } + ], + "omero": { + "name": image_key, + "channels": [ + { + "label": "channel_0", + "color": "FFFFFF", + "window": {"min": 0, "max": 4095, "start": 0, "end": 4095}, + "active": True, + } + ], + }, + }, + "spatialdata_attrs": experimental_codec_writer_attrs(), + } + + +def _base_image_element(image: Any) -> Any: + children = getattr(image, "children", None) + if children is None or "scale0" not in children: + return image + + scale0 = children["scale0"] + dataset = getattr(scale0, "ds", None) + if dataset is None: + return scale0 + if "image" in dataset: + return dataset["image"] + + data_vars = getattr(dataset, "data_vars", {}) + for name in data_vars: + return dataset[name] + raise ValueError("Could not find an image variable in SpatialData multiscale image scale0") + + +def image_to_tczyx(image: Any, dims: tuple[str, ...] | list[str] | None = None) -> np.ndarray: + """Return an image as a NumPy array with shape ``[t, c, z, y, x]``.""" + image = _base_image_element(image) + + if dims is None: + maybe_dims = getattr(image, "dims", None) + dims = tuple(str(dim) for dim in maybe_dims) if maybe_dims is not None else None + + data = getattr(image, "data", image) + if hasattr(data, "compute"): + data = data.compute() + array = np.asarray(data) + + if dims is not None: + normalized_dims = tuple(str(dim) for dim in dims) + if len(normalized_dims) != array.ndim: + raise ValueError(f"dims length {len(normalized_dims)} does not match array ndim {array.ndim}") + supported = ("t", "c", "z", "y", "x") + unsupported = [dim for dim in normalized_dims if dim not in supported] + if unsupported: + raise ValueError(f"Unsupported image dimensions: {unsupported}") + if "y" not in normalized_dims or "x" not in normalized_dims: + raise ValueError("Image dimensions must include 'y' and 'x'.") + + present = [dim for dim in supported if dim in normalized_dims] + array = np.transpose(array, [normalized_dims.index(dim) for dim in present]) + for axis_index, dim in enumerate(supported): + if dim not in present: + array = np.expand_dims(array, axis=axis_index) + return np.asarray(array) + + if array.ndim == 2: + return array.reshape(1, 1, 1, *array.shape) + if array.ndim == 3: + return array.reshape(1, array.shape[0], 1, array.shape[1], array.shape[2]) + if array.ndim == 4: + return array.reshape(1, *array.shape) + if array.ndim == 5: + return array + raise ValueError("image must have shape yx, cyx, czyx, or tczyx when dims are not provided") + + +def _is_lossless_encode(codec: str, encode_options: dict[str, Any] | None) -> bool: + if is_htj2k_codec(codec): + from spatialdata_codec_writer.htj2k_encode import openjph_encode_options + + reversible, _quality = openjph_encode_options(encode_options or {}) + return reversible + if codec == CODEC_JPEG2K: + return bool((encode_options or {}).get("reversible", True)) + raise ValueError(f"Unsupported codec: {codec}") + + +def _write_array_chunks( + store_path: Path, + array_path: str, + image: np.ndarray, + chunks: tuple[int, ...], + codec: str, + encode_options: dict[str, Any] | None = None, +) -> list[dict[str, Any]]: + is_lossless = _is_lossless_encode(codec, encode_options) + refs: list[dict[str, Any]] = [] + for coords in chunk_grid(image.shape, chunks): + chunk = _extract_chunk(image, chunks, coords) + encoded = encode_image_plane( + chunk.reshape(chunk.shape[-2], chunk.shape[-1]), codec, encode_options or {} + ) + chunk_rel = f"{array_path}/c/" + "/".join(str(c) for c in coords) + chunk_path = store_path / chunk_rel + chunk_path.parent.mkdir(parents=True, exist_ok=True) + chunk_path.write_bytes(encoded) + + expected_plane = chunk.reshape(chunk.shape[-2], chunk.shape[-1]) + if len(refs) < 4: + decoded = decode_image_plane(encoded, codec).reshape(expected_plane.shape) + if is_lossless and not np.array_equal(decoded, expected_plane): + raise RuntimeError(f"Codec self-validation failed for chunk {coords}") + sample_plane = expected_plane if is_lossless else decoded + refs.append( + { + "coords": list(coords), + "path": chunk_rel, + "encoded_sha256": sha256(encoded), + "decoded_sha256": sha256(sample_plane.tobytes()), + "samples": [ + int(sample_plane[0, 0]), + int(sample_plane[0, min(1, sample_plane.shape[1] - 1)]), + int(sample_plane[min(1, sample_plane.shape[0] - 1), 0]), + ], + } + ) + return refs + + +def _validate_codec_chunks(chunks: tuple[int, int, int, int, int]) -> None: + if len(chunks) != 5: + raise ValueError("chunks must have shape [t, c, z, y, x]") + if chunks[:3] != (1, 1, 1): + raise ValueError("v1 codec fixtures require chunks beginning with (1, 1, 1)") + + +def _multiscale_levels(base: np.ndarray, multiscale: bool) -> list[np.ndarray]: + levels = [base] + if multiscale: + levels.append(_downsample2(base)) + return levels + + +def _add_codec_image_to_store( + store_path: Path, + metadata: dict[str, Any], + *, + image_key: str, + image: Any, + codec: str, + chunks: tuple[int, int, int, int, int], + multiscale: bool, + encode_options: dict[str, Any] | None, +) -> tuple[np.ndarray, list[dict[str, Any]]]: + base = image_to_tczyx(image) + if base.ndim != 5: + raise ValueError("image must have shape [t, c, z, y, x]") + + levels = _multiscale_levels(base, multiscale) + image_attrs = _image_attrs( + [ + { + "path": str(level_index), + "coordinateTransformations": [ + {"type": "scale", "scale": [1, 1, 1, 2**level_index, 2**level_index]} + ], + } + for level_index in range(len(levels)) + ], + image_key, + ) + metadata[f"images/{image_key}"] = _group_metadata(image_attrs) + + chunk_refs: list[dict[str, Any]] = [] + for level_index, level in enumerate(levels): + array_path = f"images/{image_key}/{level_index}" + metadata[array_path] = _array_metadata(level.shape, chunks, level.dtype, codec) + chunk_refs.extend( + _write_array_chunks(store_path, array_path, level, chunks, codec, encode_options) + ) + return base, chunk_refs + + +def _finalize_codec_store(store_path: Path, metadata: dict[str, Any]) -> None: + root_metadata = { + "zarr_format": 3, + "node_type": "group", + "attributes": {"spatialdata_attrs": experimental_codec_writer_attrs()}, + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": metadata, + }, + } + write_json(store_path / "zarr.json", root_metadata) + for node_path, node_metadata in metadata.items(): + write_json(store_path / node_path / "zarr.json", node_metadata) + + +def write_codec_spatialdata_images( + path: str | Path, + *, + images: list[CodecImageWrite], + codec: CodecName = CODEC_JPEG2K, + chunks: tuple[int, int, int, int, int] = (1, 1, 1, 32, 32), + multiscale: bool = True, + overwrite: bool = False, +) -> WrittenFixture: + if not images: + raise ValueError("images must contain at least one CodecImageWrite entry.") + + _validate_codec_chunks(chunks) + store_path = Path(path) + if store_path.exists(): + if not overwrite: + raise FileExistsError(store_path) + shutil.rmtree(store_path) + store_path.mkdir(parents=True) + + metadata: dict[str, Any] = {"images": _group_metadata()} + image_manifests: list[dict[str, Any]] = [] + multiscale_levels = 2 if multiscale else 1 + + for spec in images: + if f"images/{spec.image_key}" in metadata: + raise ValueError(f"Duplicate image_key {spec.image_key!r}.") + base, chunk_refs = _add_codec_image_to_store( + store_path, + metadata, + image_key=spec.image_key, + image=spec.image, + codec=codec, + chunks=chunks, + multiscale=multiscale, + encode_options=spec.encode_options, + ) + image_entry: dict[str, Any] = { + "image_key": spec.image_key, + "image_path": f"images/{spec.image_key}", + "shape": list(base.shape), + "dtype": str(base.dtype), + "chunks_checked": chunk_refs[:4], + } + if spec.encode_options is not None: + image_entry["encode_options"] = spec.encode_options + image_entry["lossless"] = _is_lossless_encode(codec, spec.encode_options) + image_manifests.append(image_entry) + + _finalize_codec_store(store_path, metadata) + + manifest: dict[str, Any] = { + "format": "spatialdata-codec-fixture/v2", + "codec": codec, + "store": store_path.name, + "chunks": list(chunks), + "multiscale_levels": multiscale_levels, + "images": image_manifests, + "packages": { + "imagecodecs": package_version("imagecodecs"), + "numpy": package_version("numpy"), + "spatialdata": package_version("spatialdata"), + "zarr": package_version("zarr"), + }, + } + if is_htj2k_codec(codec): + manifest["encoder"] = HTJ2K_ENCODER + manifest_path = store_path.with_suffix(".manifest.json") + write_json(manifest_path, manifest) + + try: + import spatialdata as sd + + sd.read_zarr(store_path) + except Exception as exc: # pragma: no cover + manifest["spatialdata_read_warning"] = str(exc) + write_json(manifest_path, manifest) + + return WrittenFixture(store_path=store_path, manifest_path=manifest_path, manifest=manifest) + + +def write_codec_spatialdata( + path: str | Path, + *, + codec: CodecName = CODEC_JPEG2K, + image: Any | None = None, + image_key: str = "codec_image", + chunks: tuple[int, int, int, int, int] = (1, 1, 1, 32, 32), + multiscale: bool = True, + overwrite: bool = False, + encode_options: dict[str, Any] | None = None, +) -> WrittenFixture: + image_write = CodecImageWrite( + image_key=image_key, + image=image if image is not None else _default_image(), + encode_options=encode_options, + ) + written = write_codec_spatialdata_images( + path, + images=[image_write], + codec=codec, + chunks=chunks, + multiscale=multiscale, + overwrite=overwrite, + ) + image_manifest = written.manifest["images"][0] + manifest = { + **written.manifest, + "format": "spatialdata-codec-fixture/v1", + "image_path": image_manifest["image_path"], + "shape": image_manifest["shape"], + "dtype": image_manifest["dtype"], + "chunks_checked": image_manifest["chunks_checked"], + } + if "encode_options" in image_manifest: + manifest["encode_options"] = image_manifest["encode_options"] + manifest["lossless"] = image_manifest["lossless"] + del manifest["images"] + write_json(written.manifest_path, manifest) + return WrittenFixture( + store_path=written.store_path, + manifest_path=written.manifest_path, + manifest=manifest, + ) + + +def write_codec_spatialdata_image( + path: str | Path, + spatialdata_or_path: Any, + *, + image_key: str, + codec: CodecName = CODEC_JPEG2K, + chunks: tuple[int, int, int, int, int] = (1, 1, 1, 32, 32), + multiscale: bool = True, + overwrite: bool = False, +) -> WrittenFixture: + source = spatialdata_or_path + if isinstance(spatialdata_or_path, str | Path): + import spatialdata as sd + + source = sd.read_zarr(spatialdata_or_path) + + images = getattr(source, "images", None) + if images is None or image_key not in images: + raise KeyError(f"SpatialData object does not contain image {image_key!r}") + + return write_codec_spatialdata( + path, + codec=codec, + image=image_to_tczyx(images[image_key]), + image_key=image_key, + chunks=chunks, + multiscale=multiscale, + overwrite=overwrite, + ) + + +def write_jpeg2k_fixture(path: str | Path, *, overwrite: bool = False) -> WrittenFixture: + return write_codec_spatialdata(path, codec=CODEC_JPEG2K, overwrite=overwrite) diff --git a/python/spatialdata-codec-writer/scripts/generate_codec_fixtures.py b/python/spatialdata-codec-writer/scripts/generate_codec_fixtures.py new file mode 100644 index 00000000..274a0524 --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/generate_codec_fixtures.py @@ -0,0 +1,79 @@ +#!/usr/bin/env python3 +"""Generate codec test fixtures for the SpatialData.ts monorepo (dev-only).""" + +from __future__ import annotations + +import argparse +import sys +from pathlib import Path + +# Allow imports from this scripts package when run via uv/python -m +_SCRIPTS_DIR = Path(__file__).resolve().parent +_SRC_DIR = str(_SCRIPTS_DIR.parent / "src") +if _SRC_DIR not in sys.path: + sys.path.insert(0, _SRC_DIR) +if str(_SCRIPTS_DIR) not in sys.path: + sys.path.insert(0, str(_SCRIPTS_DIR)) + +from spatialdata_codec_writer.htj2k_encode import htj2k_encode_available + +from fixture_writer import write_jpeg2k_fixture +from htj2k_fixtures import ( + write_htj2k_encode_demo_fixtures, + write_htj2k_fixture, + write_htj2k_quality_sweep_manifest, +) +from mandelbulb_fixtures import write_mandelbulb_fixture + + +def _chunks(value: list[int]) -> tuple[int, int, int, int, int]: + if len(value) != 5: + raise argparse.ArgumentTypeError("chunks must contain exactly five integers: t c z y x") + return (value[0], value[1], value[2], value[3], value[4]) + + +def _generate_fixtures(args: argparse.Namespace) -> None: + output_dir = Path(args.output_dir) + output_dir.mkdir(parents=True, exist_ok=True) + + written = [write_jpeg2k_fixture(output_dir / "jpeg2k.zarr", overwrite=args.overwrite)] + if args.experimental_htj2k: + if htj2k_encode_available(): + written.append( + write_mandelbulb_fixture(output_dir / "mandelbulb.zarr", overwrite=args.overwrite) + ) + written.append(write_htj2k_fixture(output_dir / "htj2k.zarr", overwrite=args.overwrite)) + sweep_path = write_htj2k_quality_sweep_manifest( + output_dir / "htj2k-quality-sweep.manifest.json" + ) + print(f"Wrote {sweep_path}") + demo_path = write_htj2k_encode_demo_fixtures(output_dir, overwrite=args.overwrite) + print(f"Wrote {demo_path}") + else: + print( + "Skipping mandelbulb.zarr and htj2k.zarr: OpenJPH WASM HTJ2K encoder is not available.", + file=sys.stderr, + ) + + for fixture in written: + print(f"Wrote {fixture.store_path}") + print(f"Wrote {fixture.manifest_path}") + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser(description="Generate SpatialData codec test fixtures") + parser.add_argument("--output-dir", default="test-fixtures/codecs") + parser.add_argument("--overwrite", action="store_true") + parser.add_argument("--experimental-htj2k", action="store_true") + parser.set_defaults(func=_generate_fixtures) + return parser + + +def main(argv: list[str] | None = None) -> None: + parser = build_parser() + args = parser.parse_args(argv) + args.func(args) + + +if __name__ == "__main__": + main() diff --git a/python/spatialdata-codec-writer/scripts/htj2k_fixtures.py b/python/spatialdata-codec-writer/scripts/htj2k_fixtures.py new file mode 100644 index 00000000..4f7d25f7 --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/htj2k_fixtures.py @@ -0,0 +1,195 @@ +from __future__ import annotations + +from pathlib import Path +from typing import Any + +import numpy as np + +from spatialdata_codec_writer.codecs import ( + CODEC_HTJ2K_OPENJPH, + HTJ2K_ENCODER, + decode_htj2k_plane, + write_json, +) +from spatialdata_codec_writer.htj2k_encode import encode_htj2k_plane, htj2k_encode_available + +from fixture_writer import CodecImageWrite, WrittenFixture, write_codec_spatialdata, write_codec_spatialdata_images +from synthetic_images import fractal_tczyx_image, mandelbrot_plane + +HTJ2K_ENCODE_DEMO_STORE = "htj2k-demo.zarr" + +HTJ2K_QUALITY_SWEEP: tuple[dict[str, Any], ...] = ( + {"label": "lossless", "reversible": True, "quality": 0.0}, + {"label": "q0.0001", "reversible": False, "quality": 0.0001}, + {"label": "q0.0002", "reversible": False, "quality": 0.0002}, + {"label": "q0.0005", "reversible": False, "quality": 0.0005}, + {"label": "q0.001", "reversible": False, "quality": 0.001}, + {"label": "q0.002", "reversible": False, "quality": 0.002}, + {"label": "q0.005", "reversible": False, "quality": 0.005}, + {"label": "q0.01", "reversible": False, "quality": 0.01}, + {"label": "q0.05", "reversible": False, "quality": 0.05}, + {"label": "q0.1", "reversible": False, "quality": 0.1}, +) + +HTJ2K_ENCODE_DEMO_SIZE = 512 +HTJ2K_ENCODE_DEMO_CHUNKS: tuple[int, int, int, int, int] = (1, 1, 1, 64, 64) +HTJ2K_ENCODE_DEMO_PRESETS: tuple[dict[str, Any], ...] = ( + {"label": "lossless", "suffix": "lossless", "encode_options": {"reversible": True}}, + { + "label": "balanced (q=0.0002)", + "suffix": "balanced", + "encode_options": {"reversible": False, "quality": 0.0002}, + }, + { + "label": "small (q=0.001)", + "suffix": "small", + "encode_options": {"reversible": False, "quality": 0.001}, + }, +) + + +def htj2k_encode_demo_image_key(suffix: str) -> str: + return f"mandelbrot_{suffix}" + + +def _count_image_encoded_bytes(store_path: Path, image_key: str) -> int: + encoded_bytes = 0 + image_root = store_path / "images" / image_key + for level_dir in image_root.iterdir(): + if not level_dir.is_dir(): + continue + c_dir = level_dir / "c" + if not c_dir.is_dir(): + continue + for chunk_path in c_dir.rglob("*"): + if chunk_path.is_file(): + encoded_bytes += chunk_path.stat().st_size + return encoded_bytes + + +def write_htj2k_fixture(path: str | Path, *, overwrite: bool = False) -> WrittenFixture: + return write_codec_spatialdata( + path, + codec=CODEC_HTJ2K_OPENJPH, + image=fractal_tczyx_image(), + overwrite=overwrite, + ) + + +def write_htj2k_encode_demo_fixtures(path: str | Path, *, overwrite: bool = False) -> Path: + output_dir = Path(path) + output_dir.mkdir(parents=True, exist_ok=True) + store_path = output_dir / HTJ2K_ENCODE_DEMO_STORE + image = fractal_tczyx_image(HTJ2K_ENCODE_DEMO_SIZE) + + image_writes = [ + CodecImageWrite( + image_key=htj2k_encode_demo_image_key(str(preset["suffix"])), + image=image, + encode_options=dict(preset["encode_options"]), + ) + for preset in HTJ2K_ENCODE_DEMO_PRESETS + ] + written = write_codec_spatialdata_images( + store_path, + images=image_writes, + codec=CODEC_HTJ2K_OPENJPH, + chunks=HTJ2K_ENCODE_DEMO_CHUNKS, + multiscale=True, + overwrite=overwrite, + ) + + variants: list[dict[str, Any]] = [] + for preset, spec in zip(HTJ2K_ENCODE_DEMO_PRESETS, image_writes, strict=True): + suffix = str(preset["suffix"]) + encode_options = dict(preset["encode_options"]) + image_key = spec.image_key + image_manifest = next( + entry for entry in written.manifest["images"] if entry["image_key"] == image_key + ) + encoded_bytes = _count_image_encoded_bytes(store_path, image_key) + variants.append( + { + "label": preset["label"], + "suffix": suffix, + "image_key": image_key, + "image_path": image_manifest["image_path"], + "lossless": image_manifest.get("lossless", False), + "encode_options": encode_options, + "encoded_bytes": encoded_bytes, + "compression_ratio": int(image.nbytes) / encoded_bytes if encoded_bytes else None, + } + ) + + manifest_path = output_dir / "htj2k-encode-demo.manifest.json" + write_json( + manifest_path, + { + "format": "spatialdata-htj2k-encode-demo/v2", + "encoder": HTJ2K_ENCODER, + "store": HTJ2K_ENCODE_DEMO_STORE, + "image": { + "kind": "mandelbrot", + "shape": list(image.shape), + "dtype": str(image.dtype), + }, + "chunks": list(HTJ2K_ENCODE_DEMO_CHUNKS), + "multiscale_levels": written.manifest["multiscale_levels"], + "variants": variants, + }, + ) + return manifest_path + + +def _plane_error_metrics(source: np.ndarray, decoded: np.ndarray) -> dict[str, float]: + diff = decoded.astype(np.float64) - source.astype(np.float64) + mse = float(np.mean(diff * diff)) + return { + "rmse": float(np.sqrt(mse)), + "max_abs_error": float(np.max(np.abs(diff))), + } + + +def write_htj2k_quality_sweep_manifest(path: str | Path) -> Path: + if not htj2k_encode_available(): + raise RuntimeError("OpenJPH WASM HTJ2K encoder is not available.") + + plane = mandelbrot_plane(64) + raw_bytes = int(plane.nbytes) + qualities: list[dict[str, Any]] = [] + for entry in HTJ2K_QUALITY_SWEEP: + encoded = encode_htj2k_plane( + plane, + reversible=bool(entry["reversible"]), + quality=float(entry["quality"]), + ) + decoded = decode_htj2k_plane(encoded).reshape(plane.shape) + metrics = _plane_error_metrics(plane, decoded) + qualities.append( + { + **entry, + "encoded_bytes": len(encoded), + "compression_ratio": raw_bytes / len(encoded), + **metrics, + } + ) + + manifest_path = Path(path) + manifest_path.parent.mkdir(parents=True, exist_ok=True) + write_json( + manifest_path, + { + "format": "spatialdata-htj2k-quality-sweep/v1", + "encoder": HTJ2K_ENCODER, + "api": "HTJ2KEncoder.setQuality(reversible, quality)", + "quality_note": ( + "OpenJPH WASM quality is a quantization factor, not JP2K-style 0-100. " + "Lower values preserve more detail (larger output). Integer values above " + "~15 with irreversible=true produce degenerate minimum-bitrate output." + ), + "image": {"kind": "mandelbrot", "shape": list(plane.shape), "dtype": str(plane.dtype)}, + "raw_bytes": raw_bytes, + "qualities": qualities, + }, + ) + return manifest_path diff --git a/python/spatialdata-codec-writer/scripts/mandelbulb_fixtures.py b/python/spatialdata-codec-writer/scripts/mandelbulb_fixtures.py new file mode 100644 index 00000000..f9892afe --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/mandelbulb_fixtures.py @@ -0,0 +1,39 @@ +from __future__ import annotations + +from pathlib import Path + +from spatialdata_codec_writer.codecs import CODEC_HTJ2K_OPENJPH + +from fixture_writer import WrittenFixture, write_codec_spatialdata +from synthetic_images import volume_tczyx + +MANDELBULB_FIXTURE_SIZE = 128 +MANDELBULB_FIXTURE_T = 2 +MANDELBULB_FIXTURE_C = 1 +MANDELBULB_FIXTURE_Z = 8 +MANDELBULB_FIXTURE_CHUNKS: tuple[int, int, int, int, int] = (1, 1, 1, 128, 128) +MANDELBULB_FIXTURE_IMAGE_KEY = "mandelbulb" +MANDELBULB_ENCODE_OPTIONS = {"reversible": True} + + +def mandelbulb_fixture_volume(): + return volume_tczyx( + MANDELBULB_FIXTURE_SIZE, + t=MANDELBULB_FIXTURE_T, + c=MANDELBULB_FIXTURE_C, + z=MANDELBULB_FIXTURE_Z, + pattern="mandelbulb", + ) + + +def write_mandelbulb_fixture(path: str | Path, *, overwrite: bool = False) -> WrittenFixture: + return write_codec_spatialdata( + path, + codec=CODEC_HTJ2K_OPENJPH, + image=mandelbulb_fixture_volume(), + image_key=MANDELBULB_FIXTURE_IMAGE_KEY, + chunks=MANDELBULB_FIXTURE_CHUNKS, + multiscale=False, + encode_options=MANDELBULB_ENCODE_OPTIONS, + overwrite=overwrite, + ) diff --git a/python/spatialdata-codec-writer/scripts/provenance.py b/python/spatialdata-codec-writer/scripts/provenance.py new file mode 100644 index 00000000..b049fe51 --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/provenance.py @@ -0,0 +1,25 @@ +"""Experimental provenance marker for codec test fixtures (not spatialdata.write() artifacts).""" + +from __future__ import annotations + +from importlib import metadata + +EXPERIMENTAL_CODEC_WRITER_VERSION = "0.1.0" +DEFAULT_SPATIALDATA_VERSION = "0.7.2" + + +def _spatialdata_version() -> str: + try: + return metadata.version("spatialdata") + except metadata.PackageNotFoundError: + return DEFAULT_SPATIALDATA_VERSION + + +def experimental_codec_writer_attrs() -> dict[str, str]: + return { + # readZarr validates raster attrs against spatialDataAttrsSchema, which + # requires a spatialdata library version even for experimental fixtures. + "version": _spatialdata_version(), + "experimental_codec_writer": EXPERIMENTAL_CODEC_WRITER_VERSION, + "note": "codec test fixture; not a spatialdata.write() artifact", + } diff --git a/python/spatialdata-codec-writer/scripts/synthetic_images.py b/python/spatialdata-codec-writer/scripts/synthetic_images.py new file mode 100644 index 00000000..d427f97b --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/synthetic_images.py @@ -0,0 +1,128 @@ +from __future__ import annotations + +from typing import Literal + +import numpy as np + +MANDELBROT_MAX_ITER = 255 +MANDELBULB_MAX_ITER = 8 +MANDELBULB_POWER = 8 + + +def mandelbrot_plane(size: int) -> np.ndarray: + """Return a uint16 Mandelbrot escape-time plane as a basic visual quality test.""" + x = np.arange(size, dtype=np.float64) + y = np.arange(size, dtype=np.float64) + cr = (x / size) * 3.5 - 2.5 + ci = (y / size) * 2.0 - 1.0 + cr_grid, ci_grid = np.meshgrid(cr, ci) + + zr = np.zeros_like(cr_grid) + zi = np.zeros_like(ci_grid) + iteration = np.zeros(cr_grid.shape, dtype=np.int32) + mask = np.ones(cr_grid.shape, dtype=bool) + + for _ in range(MANDELBROT_MAX_ITER): + if not np.any(mask): + break + zr2 = zr * zr + zi2 = zi * zi + nr = zr2 - zi2 + cr_grid + new_zi = 2.0 * zr * zi + ci_grid + zr = np.where(mask, nr, zr) + zi = np.where(mask, new_zi, zi) + iteration[mask] += 1 + mask &= zr * zr + zi * zi <= 4.0 + + return ((iteration * 16) % 4096).astype(np.uint16) + + +def _indexed_plane(size: int, *, t: int, c: int, z: int) -> np.ndarray: + y, x = np.mgrid[0:size, 0:size] + return (t * 1000 + c * 100 + z * 10 + y + x).astype(np.uint16) + + +def _mandelbulb_plane( + size: int, + *, + z: int, + z_count: int, + t: int = 0, +) -> np.ndarray: + """Sample a lightweight Mandelbulb escape-time field on a y/x plane at fixed z.""" + y_coords = np.linspace(-1.0, 1.0, size, dtype=np.float64) + x_coords = np.linspace(-1.5, 1.0, size, dtype=np.float64) + z_coord = (z / max(z_count - 1, 1)) * 2.0 - 1.0 + t * 0.05 + + yy, xx = np.meshgrid(y_coords, x_coords, indexing="ij") + cx = xx + cy = yy + cz = np.full_like(xx, z_coord) + + zx = np.zeros_like(cx) + zy = np.zeros_like(cy) + zz = np.zeros_like(cz) + iteration = np.zeros(cx.shape, dtype=np.int32) + mask = np.ones(cx.shape, dtype=bool) + + for step in range(MANDELBULB_MAX_ITER): + if not np.any(mask): + break + r = np.sqrt(zx * zx + zy * zy + zz * zz) + iteration[mask & (r >= 2.0)] = step + mask &= r < 2.0 + if not np.any(mask): + break + + theta = np.arctan2(np.sqrt(zx * zx + zy * zy), zz) + phi = np.arctan2(zy, zx) + rn = np.zeros_like(r) + rn[mask] = np.power(r[mask], MANDELBULB_POWER) + sin_theta = np.sin(MANDELBULB_POWER * theta) + cos_theta = np.cos(MANDELBULB_POWER * theta) + sin_phi = np.sin(MANDELBULB_POWER * phi) + cos_phi = np.cos(MANDELBULB_POWER * phi) + + new_zx = rn * sin_theta * cos_phi + cx + new_zy = rn * sin_theta * sin_phi + cy + new_zz = rn * cos_theta + cz + zx = np.where(mask, new_zx, zx) + zy = np.where(mask, new_zy, zy) + zz = np.where(mask, new_zz, zz) + + iteration[mask] = MANDELBULB_MAX_ITER + + return ((iteration * 16) % 4096).astype(np.uint16) + + +def volume_tczyx( + size: int = 64, + *, + t: int = 1, + c: int = 1, + z: int = 1, + pattern: Literal["mandelbulb", "indexed"] = "mandelbulb", +) -> np.ndarray: + """Return a synthetic volume with shape ``[t, c, z, y, x]``.""" + if t < 1 or c < 1 or z < 1 or size < 1: + raise ValueError("t, c, z, and size must be positive integers.") + if pattern not in ("mandelbulb", "indexed"): + raise ValueError( + f"Unsupported pattern {pattern!r}; expected 'mandelbulb' or 'indexed'." + ) + + volume = np.zeros((t, c, z, size, size), dtype=np.uint16) + for t_index in range(t): + for c_index in range(c): + for z_index in range(z): + if pattern == "indexed": + plane = _indexed_plane(size, t=t_index, c=c_index, z=z_index) + else: + plane = _mandelbulb_plane(size, z=z_index, z_count=z, t=t_index) + volume[t_index, c_index, z_index] = plane + return volume + + +def fractal_tczyx_image(size: int = 64) -> np.ndarray: + """Return a Mandelbrot raster with shape ``[t, c, z, y, x]``.""" + return mandelbrot_plane(size).reshape(1, 1, 1, size, size) diff --git a/python/spatialdata-codec-writer/scripts/write_synthetic.py b/python/spatialdata-codec-writer/scripts/write_synthetic.py new file mode 100644 index 00000000..2d4d6711 --- /dev/null +++ b/python/spatialdata-codec-writer/scripts/write_synthetic.py @@ -0,0 +1,189 @@ +#!/usr/bin/env python3 +"""Write a synthetic tczyx volume as a SpatialData codec store.""" + +from __future__ import annotations + +import argparse +import json +import sys +from pathlib import Path +from typing import Any + +_SCRIPTS_DIR = Path(__file__).resolve().parent +_SRC_DIR = str(_SCRIPTS_DIR.parent / "src") +if _SRC_DIR not in sys.path: + sys.path.insert(0, _SRC_DIR) +if str(_SCRIPTS_DIR) not in sys.path: + sys.path.insert(0, str(_SCRIPTS_DIR)) + +from spatialdata_codec_writer.codecs import CODEC_HTJ2K_OPENJPH, CODEC_JPEG2K, CodecName +from spatialdata_codec_writer.htj2k_encode import htj2k_encode_available + +from fixture_writer import WrittenFixture, write_codec_spatialdata +from synthetic_images import fractal_tczyx_image, mandelbrot_plane, volume_tczyx + + +def _positive_int(value: str) -> int: + parsed = int(value) + if parsed <= 0: + raise argparse.ArgumentTypeError("must be a positive integer") + return parsed + + +def _tczyx_chunks(values: list[int]) -> tuple[int, int, int, int, int]: + if len(values) != 5: + raise argparse.ArgumentTypeError("chunks must contain exactly five integers: t c z y x") + return (values[0], values[1], values[2], values[3], values[4]) + + +def _default_spatial_chunk(size: int) -> int: + if size >= 512: + return 256 + if size >= 128: + return 128 + return max(32, size) + + +def _build_volume(args: argparse.Namespace): + pattern = args.pattern + if pattern == "mandelbrot": + plane = mandelbrot_plane(args.size) + return plane.reshape(1, 1, 1, args.size, args.size) + if pattern == "fractal": + return fractal_tczyx_image(args.size) + return volume_tczyx( + args.size, + t=args.t, + c=args.c, + z=args.z, + pattern=pattern, + ) + + +def _encode_options(args: argparse.Namespace) -> dict[str, Any] | None: + if args.codec != CODEC_HTJ2K_OPENJPH: + return None + if args.preset == "lossless" or args.reversible: + return {"reversible": True} + if args.quality is not None: + return {"reversible": False, "quality": args.quality} + preset_quality = {"balanced": 0.0002, "small": 0.001}.get(args.preset) + if preset_quality is not None: + return {"reversible": False, "quality": preset_quality} + return {"reversible": True} + + +def _write(args: argparse.Namespace) -> WrittenFixture: + if args.codec == CODEC_HTJ2K_OPENJPH and not htj2k_encode_available(): + raise SystemExit( + "HTJ2K encode is not available. Install Node.js on PATH and vendor OpenJPH " + "(node scripts/vendor-openjph-for-python.mjs from the monorepo root)." + ) + + if args.quality is not None and args.reversible: + raise SystemExit("error: --quality cannot be used with --reversible") + if args.quality is not None and args.codec != CODEC_HTJ2K_OPENJPH: + raise SystemExit("error: --quality is for HTJ2K only") + + volume = _build_volume(args) + chunks = args.chunks or ( + 1, + 1, + 1, + args.chunk_spatial, + args.chunk_spatial, + ) + + return write_codec_spatialdata( + args.output, + codec=args.codec, + image=volume, + image_key=args.image_key, + chunks=chunks, + multiscale=args.multiscale, + encode_options=_encode_options(args), + overwrite=args.overwrite, + ) + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description="Generate and write a synthetic SpatialData codec image store", + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + ) + parser.add_argument("output", type=Path, help="Output .zarr store path") + parser.add_argument( + "--pattern", + choices=["mandelbulb", "indexed", "mandelbrot", "fractal"], + default="mandelbulb", + help="Synthetic pattern (mandelbulb/indexed are multi-dimensional volumes)", + ) + parser.add_argument("--size", type=_positive_int, default=128, help="Square y/x plane size") + parser.add_argument("--t", type=_positive_int, default=1, help="Time axis length") + parser.add_argument("--c", type=_positive_int, default=1, help="Channel axis length") + parser.add_argument("--z", type=_positive_int, default=1, help="Z axis length") + parser.add_argument("--image-key", default="synthetic", help="SpatialData image key") + parser.add_argument( + "--codec", + choices=[CODEC_JPEG2K, CODEC_HTJ2K_OPENJPH], + default=CODEC_HTJ2K_OPENJPH, + help="Image codec id", + ) + parser.add_argument( + "--preset", + choices=["lossless", "balanced", "small"], + default="lossless", + help="HTJ2K preset (ignored for JPEG2K)", + ) + parser.add_argument( + "--quality", + type=float, + metavar="Q", + help="HTJ2K quantization factor (implies lossy; overrides --preset)", + ) + parser.add_argument( + "--reversible", + action="store_true", + help="Force lossless HTJ2K (default for lossless preset)", + ) + parser.add_argument( + "--chunk-spatial", + type=_positive_int, + help="Square y/x chunk size when --chunks is omitted (default depends on --size)", + ) + parser.add_argument( + "--chunks", + type=int, + nargs=5, + metavar=("T", "C", "Z", "Y", "X"), + help="Explicit tczyx chunk shape", + ) + parser.add_argument("--multiscale", action="store_true", help="Write a 2× downsampled pyramid level") + parser.add_argument("--overwrite", action="store_true", help="Replace an existing store") + parser.set_defaults(func=_write) + return parser + + +def _normalize_argv(argv: list[str] | None) -> list[str]: + if argv is None: + argv = sys.argv[1:] + if argv and argv[0] == "--": + argv = argv[1:] + return argv + + +def main(argv: list[str] | None = None) -> None: + parser = build_parser() + args = parser.parse_args(_normalize_argv(argv)) + if args.chunk_spatial is None: + args.chunk_spatial = _default_spatial_chunk(args.size) + if args.chunks is not None: + args.chunks = _tczyx_chunks(list(args.chunks)) + written = args.func(args) + print(json.dumps(written.manifest, indent=2, sort_keys=True)) + print(f"Wrote {written.store_path}", file=sys.stderr) + print(f"Wrote {written.manifest_path}", file=sys.stderr) + + +if __name__ == "__main__": + main() diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/__init__.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/__init__.py new file mode 100644 index 00000000..69e02756 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/__init__.py @@ -0,0 +1,29 @@ +from .recompress import ( + HTJ2K_PRESETS, + JP2K_PRESETS, + RecompressedSpatialData, + recompress_spatialdata, + resolve_recompression_config, +) +from .codecs import ( + CODEC_HTJ2K_LEGACY, + CODEC_HTJ2K_OPENJPH, + CODEC_JPEG2K, + HTJ2K_ENCODER, + is_htj2k_codec, +) +from .htj2k_encode import htj2k_encode_available + +__all__ = [ + "CODEC_HTJ2K_LEGACY", + "CODEC_HTJ2K_OPENJPH", + "CODEC_JPEG2K", + "HTJ2K_PRESETS", + "HTJ2K_ENCODER", + "JP2K_PRESETS", + "RecompressedSpatialData", + "htj2k_encode_available", + "is_htj2k_codec", + "recompress_spatialdata", + "resolve_recompression_config", +] diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/cli.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/cli.py new file mode 100644 index 00000000..02376d66 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/cli.py @@ -0,0 +1,137 @@ +from __future__ import annotations + +import argparse +import json +import os +from pathlib import Path + +from .recompress import recompress_spatialdata + + +def _recompress_chunks(value: list[str] | None): + if value is None: + return None + if len(value) == 1 and value[0] == "auto": + return "auto" + try: + return tuple(int(part) for part in value) + except ValueError as exc: + raise argparse.ArgumentTypeError("chunks must be 'auto' or integer axis sizes") from exc + + +def _positive_int(value: str) -> int: + parsed = int(value) + if parsed <= 0: + raise argparse.ArgumentTypeError("--workers must be a positive integer") + return parsed + + +def _recompress(args: argparse.Namespace) -> None: + if args.quality is not None and args.reversible: + raise SystemExit("error: --quality cannot be used with --reversible") + if args.quality is not None and args.codec != "experimental.openjph_htj2k": + raise SystemExit( + "error: --quality is for HTJ2K only; use --codec experimental.openjph_htj2k" + ) + + result = recompress_spatialdata( + args.source, + args.dest, + config=args.config, + overwrite=args.overwrite, + image_key=args.image_key, + codec=args.codec, + preset=args.preset, + chunks=_recompress_chunks(args.chunks), + quality=args.quality, + reversible=True if args.reversible else None, + sibling=args.sibling, + workers=args.workers, + ) + print(json.dumps(result.manifest, indent=2, sort_keys=True)) + + +def _inspect(args: argparse.Namespace) -> None: + manifest_path = Path(args.path) + if manifest_path.is_dir(): + manifest_path = manifest_path.with_suffix(".manifest.json") + print(manifest_path.read_text()) + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description="Recompress SpatialData/OME-Zarr image stores with optional codecs" + ) + subparsers = parser.add_subparsers(dest="command", required=True) + + recompress = subparsers.add_parser("recompress") + recompress.add_argument("source", help="Existing SpatialData Zarr store") + recompress.add_argument("dest", help="Output SpatialData Zarr store") + recompress.add_argument("--config", help="JSON recompression config") + recompress.add_argument( + "--image-key", + help="Apply convenience flags to one image only (default: all images)", + ) + recompress.add_argument( + "--codec", + choices=["imagecodecs_jpeg2k", "experimental.openjph_htj2k"], + help="Image codec (all images unless --image-key is set)", + ) + recompress.add_argument( + "--preset", + choices=["lossless", "balanced", "small"], + help="Named image preset (ignored when --quality is set)", + ) + recompress.add_argument( + "--quality", + type=float, + metavar="Q", + help=( + "HTJ2K quantization factor (lower = better fidelity, larger output). " + "Implies lossy encoding; use with --codec experimental.openjph_htj2k. " + "Overrides preset quality." + ), + ) + recompress.add_argument( + "--reversible", + action="store_true", + help="Force lossless HTJ2K (cannot be combined with --quality)", + ) + recompress.add_argument( + "--chunks", + nargs="+", + metavar="CHUNK", + help="Use 'auto' or pass one integer per raster axis", + ) + recompress.add_argument("--overwrite", action="store_true") + recompress.add_argument( + "--sibling", + action="store_true", + help=( + "Write compressed images as new sibling groups (e.g. morphology_focus:jp2k_lossless) " + "instead of replacing the originals in-place" + ), + ) + recompress.add_argument( + "--workers", + type=_positive_int, + default=os.cpu_count() or 1, + help="Parallel encoder workers (default: CPU count)", + ) + recompress.set_defaults(func=_recompress) + + inspect = subparsers.add_parser("inspect") + inspect.add_argument("path") + inspect.set_defaults(func=_inspect) + + return parser + + +def main(argv: list[str] | None = None) -> None: + parser = build_parser() + args = parser.parse_args(argv) + args.func(args) + + +if __name__ == "__main__": + main() diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/codecs.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/codecs.py new file mode 100644 index 00000000..7156aa88 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/codecs.py @@ -0,0 +1,120 @@ +from __future__ import annotations + +import hashlib +import json +from importlib import metadata +from pathlib import Path +from typing import Any, Literal + +import imagecodecs +import numpy as np + +CODEC_JPEG2K = "imagecodecs_jpeg2k" +CODEC_HTJ2K_OPENJPH = "experimental.openjph_htj2k" +# Legacy label for stores written before OpenJPH WASM became the supported encoder. +CODEC_HTJ2K_LEGACY = "experimental.imagecodecs_htj2k" +HTJ2K_CODECS = frozenset({CODEC_HTJ2K_OPENJPH, CODEC_HTJ2K_LEGACY}) +HTJ2K_ENCODER = "openjph-wasm" + +CodecName = Literal["imagecodecs_jpeg2k", "experimental.openjph_htj2k"] + + +def is_htj2k_codec(codec: str) -> bool: + return codec in HTJ2K_CODECS + + +def package_version(name: str) -> str | None: + try: + return metadata.version(name) + except metadata.PackageNotFoundError: + return None + + +def json_bytes(value: dict[str, Any]) -> bytes: + return json.dumps(value, indent=2, sort_keys=True).encode("utf-8") + + +def write_json(path: Path, value: dict[str, Any]) -> None: + path.parent.mkdir(parents=True, exist_ok=True) + path.write_bytes(json_bytes(value)) + + +def sha256(data: bytes | bytearray) -> str: + return hashlib.sha256(data).hexdigest() + + +def decode_htj2k_plane(encoded: bytes | bytearray) -> np.ndarray: + """Decode an HTJ2K plane for validation (native imagecodecs when available).""" + htj2k = getattr(imagecodecs, "HTJ2K", None) + if htj2k is not None and getattr(htj2k, "available", False): + decoder = getattr(imagecodecs, "htj2k_decode", None) + if decoder is not None: + return decoder(encoded) + return imagecodecs.jpeg2k_decode(encoded) + + +def decode_image_plane(encoded: bytes | bytearray, codec: str) -> np.ndarray: + if codec == CODEC_JPEG2K: + return imagecodecs.jpeg2k_decode(encoded) + if is_htj2k_codec(codec): + return decode_htj2k_plane(encoded) + raise ValueError(f"Unsupported image codec: {codec}") + + +def encode_htj2k_plane_with_options( + plane: np.ndarray, encode_options: dict[str, Any] | None = None +) -> bytes | bytearray: + from .htj2k_encode import encode_htj2k_plane, htj2k_encode_available, openjph_encode_options + + if not htj2k_encode_available(): + raise RuntimeError( + "HTJ2K encode is not available. Install spatialdata-codec-writer with Node.js on PATH." + ) + reversible, quality = openjph_encode_options(encode_options or {}) + return encode_htj2k_plane(plane, reversible=reversible, quality=quality) + + +def encode_image_plane( + plane: np.ndarray, codec: str, encode_options: dict[str, Any] +) -> bytes | bytearray: + array = np.asarray(plane) + if codec == CODEC_JPEG2K: + return imagecodecs.jpeg2k_encode(array, **encode_options) + if codec == CODEC_HTJ2K_OPENJPH: + return encode_htj2k_plane_with_options(array, encode_options) + raise ValueError(f"Unsupported image codec: {codec}") + + +def chunk_grid(shape: tuple[int, ...], chunks: tuple[int, ...]) -> list[tuple[int, ...]]: + if len(shape) != len(chunks): + raise ValueError( + f"shape and chunks must have the same length (got {len(shape)} and {len(chunks)})" + ) + ranges = [range((size + chunk - 1) // chunk) for size, chunk in zip(shape, chunks)] + out: list[tuple[int, ...]] = [()] + for values in ranges: + out = [(*prefix, value) for prefix in out for value in values] + return out + + +def chunk_slices( + shape: tuple[int, ...], chunks: tuple[int, ...], coords: tuple[int, ...] +) -> tuple[slice, ...]: + if not (len(shape) == len(chunks) == len(coords)): + raise ValueError( + "shape, chunks, and coords must have the same length " + f"(got {len(shape)}, {len(chunks)}, and {len(coords)})" + ) + slices = [] + for coord, chunk, size in zip(coords, chunks, shape): + start = coord * chunk + slices.append(slice(start, min(start + chunk, size))) + return tuple(slices) + + +def pad_chunk(chunk: np.ndarray, chunks: tuple[int, ...]) -> np.ndarray: + if chunk.shape == chunks: + return chunk + padded = np.zeros(chunks, dtype=chunk.dtype) + padded[tuple(slice(0, size) for size in chunk.shape)] = chunk + return padded diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/htj2k_encode.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/htj2k_encode.py new file mode 100644 index 00000000..ecafb469 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/htj2k_encode.py @@ -0,0 +1,211 @@ +from __future__ import annotations + +import atexit +import base64 +import json +import os +import shutil +import struct +import subprocess +import threading +from functools import lru_cache +from pathlib import Path +from typing import Any + +import numpy as np + +_VENDOR_DIR = Path(__file__).resolve().parent / "vendor" +_ENCODE_SCRIPT = _VENDOR_DIR / "encode-plane.mjs" + + +def encode_script_path() -> Path: + return _ENCODE_SCRIPT + + +def openjph_vendor_dir() -> Path: + return _VENDOR_DIR / "openjph" + + +def openjph_encode_options(encode_options: dict[str, Any]) -> tuple[bool, float]: + """Map encode options to OpenJPH WASM setQuality(reversible, quality).""" + reversible = bool(encode_options.get("reversible", True)) + if reversible: + return True, 0.0 + quality = encode_options.get("quality", encode_options.get("level", 0.0002)) + return False, float(quality) + + +def _plane_request_payload( + plane: np.ndarray, *, reversible: bool, quality: float +) -> dict[str, Any]: + array = np.ascontiguousarray(np.asarray(plane)) + if array.ndim != 2: + raise ValueError(f"HTJ2K encode expects a 2D plane, got shape {array.shape}.") + height, width = (int(value) for value in array.shape) + return { + "width": width, + "height": height, + "dtype": array.dtype.name, + "reversible": reversible, + "quality": quality, + "plane": base64.b64encode(array.tobytes(order="C")).decode("ascii"), + } + + +class OpenJphEncoderWorker: + """Long-lived Node subprocess that loads OpenJPH WASM once.""" + + def __init__(self) -> None: + node = shutil.which("node") + if node is None: + raise RuntimeError("Node.js is required for HTJ2K encode but was not found on PATH.") + if not _ENCODE_SCRIPT.is_file(): + raise RuntimeError(f"HTJ2K encode script not found: {_ENCODE_SCRIPT}") + if not (openjph_vendor_dir() / "openjphjs.wasm").is_file(): + raise RuntimeError( + f"Vendored OpenJPH WASM not found under {openjph_vendor_dir()}. " + "Run scripts/vendor-openjph-for-python.mjs before building the package." + ) + + self._lock = threading.Lock() + self._proc = subprocess.Popen( + [node, str(_ENCODE_SCRIPT), "--worker"], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.DEVNULL, + bufsize=0, + ) + if self._proc.stdin is None or self._proc.stdout is None: + raise RuntimeError("Failed to open pipes for HTJ2K encoder worker.") + + def close(self) -> None: + with self._lock: + assert(self._proc) + if self._proc.stdin is not None: + self._proc.stdin.close() + if self._proc.poll() is None: + self._proc.wait(timeout=5) + if self._proc.poll() is None: + self._proc.terminate() + self._proc.wait(timeout=5) + if self._proc.poll() is None: + self._proc.kill() + self._proc = None # type: ignore[assignment] + + def encode_plane( + self, plane: np.ndarray, *, reversible: bool = True, quality: float = 0.0 + ) -> bytes: + with self._lock: + if self._proc is None or self._proc.poll() is not None: + raise RuntimeError("HTJ2K encoder worker is not running.") + payload = json.dumps( + _plane_request_payload(plane, reversible=reversible, quality=quality) + ).encode("utf-8") + assert self._proc.stdin is not None + assert self._proc.stdout is not None + self._proc.stdin.write(struct.pack(">I", len(payload))) + self._proc.stdin.write(payload) + self._proc.stdin.flush() + + header = self._read_exact(self._proc.stdout, 5) + status = header[0] + length = struct.unpack(">I", header[1:5])[0] + body = self._read_exact(self._proc.stdout, length) + if status != 0: + message = body.decode("utf-8", errors="replace") + raise RuntimeError(message or "HTJ2K encode failed.") + return bytes(body) + + @staticmethod + def _read_exact(stream: Any, length: int) -> bytes: + chunks: list[bytes] = [] + received = 0 + while received < length: + chunk = stream.read(length - received) + if not chunk: + raise RuntimeError("HTJ2K encoder worker closed stdout unexpectedly.") + chunks.append(chunk) + received += len(chunk) + return b"".join(chunks) + + +class EncoderPool: + """Pool of persistent OpenJPH encoder workers.""" + + def __init__(self, workers: int | None = None) -> None: + count = workers if workers is not None else (os.cpu_count() or 1) + self._workers = [OpenJphEncoderWorker() for _ in range(max(1, count))] + self._next = 0 + self._lock = threading.Lock() + + def encode_plane( + self, plane: np.ndarray, *, reversible: bool = True, quality: float = 0.0 + ) -> bytes: + with self._lock: + worker = self._workers[self._next] + self._next = (self._next + 1) % len(self._workers) + return worker.encode_plane(plane, reversible=reversible, quality=quality) + + def close(self) -> None: + for worker in self._workers: + worker.close() + + +_pool: EncoderPool | None = None +_pool_lock = threading.Lock() +_pool_workers: int | None = None + + +def configure_encoder_pool(workers: int | None = None) -> None: + """Configure or replace the global HTJ2K encoder worker pool.""" + global _pool, _pool_workers + with _pool_lock: + if _pool is not None: + _pool.close() + _pool = None + _pool_workers = workers + + +def get_encoder_pool(workers: int | None = None) -> EncoderPool: + global _pool, _pool_workers + with _pool_lock: + effective_workers = workers if workers is not None else _pool_workers + if _pool is None or (workers is not None and workers != _pool_workers): + if _pool is not None: + _pool.close() + _pool_workers = effective_workers + _pool = EncoderPool(workers=effective_workers) + return _pool + + +def shutdown_encoder_pool() -> None: + global _pool, _pool_workers + with _pool_lock: + if _pool is not None: + _pool.close() + _pool = None + _pool_workers = None + + +atexit.register(shutdown_encoder_pool) + + +@lru_cache(maxsize=1) +def htj2k_encode_available() -> bool: + """Return whether the vendored OpenJPH WASM encode helper is usable.""" + try: + plane = np.zeros((4, 4), dtype=np.uint16) + encode_htj2k_plane(plane, reversible=True, quality=0.0) + except Exception: + return False + return True + + +def encode_htj2k_plane( + plane: np.ndarray, + *, + reversible: bool = True, + quality: float = 0.0, +) -> bytes: + """Encode one 2D plane through the vendored OpenJPH WASM worker pool.""" + return get_encoder_pool().encode_plane(plane, reversible=reversible, quality=quality) diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/recompress.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/recompress.py new file mode 100644 index 00000000..1da798f2 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/recompress.py @@ -0,0 +1,714 @@ +from __future__ import annotations + +import json +import shutil +import tempfile +from concurrent.futures import ThreadPoolExecutor, as_completed +from dataclasses import dataclass +from pathlib import Path +from typing import Any, Literal + +import numpy as np +import zarr +from zarr.codecs import BloscCodec, BloscShuffle + +from .codecs import ( + CODEC_HTJ2K_OPENJPH, + CODEC_JPEG2K, + HTJ2K_ENCODER, + chunk_grid, + chunk_slices, + decode_image_plane, + encode_image_plane, + is_htj2k_codec, + package_version, + pad_chunk, + sha256, + write_json, +) +from .htj2k_encode import configure_encoder_pool, htj2k_encode_available + +ImagePreset = Literal["lossless", "balanced", "small"] +ChunkSpec = Literal["auto"] | tuple[int, ...] | list[int] + +SUPPORTED_IMAGE_CODECS = frozenset({CODEC_JPEG2K, CODEC_HTJ2K_OPENJPH}) + +SUPPORTED_BROWSER_JP2K_DTYPES = { + np.dtype("uint8"), + np.dtype("int8"), + np.dtype("uint16"), + np.dtype("int16"), +} + +JP2K_PRESETS: dict[ImagePreset, dict[str, Any]] = { + "lossless": {"reversible": True}, + "balanced": {"reversible": False, "level": 100}, + "small": {"reversible": False, "level": 75}, +} + +HTJ2K_PRESETS: dict[ImagePreset, dict[str, Any]] = { + "lossless": {"reversible": True}, + "balanced": {"reversible": False, "quality": 0.0002}, + "small": {"reversible": False, "quality": 0.001}, +} + + +@dataclass(frozen=True) +class RecompressedSpatialData: + store_path: Path + manifest_path: Path | None + manifest: dict[str, Any] + + +def _read_json(path: Path) -> dict[str, Any]: + return json.loads(path.read_text()) + + +def _load_config(config: str | Path | dict[str, Any] | None) -> dict[str, Any]: + if config is None: + return {} + if isinstance(config, dict): + return json.loads(json.dumps(config)) + return _read_json(Path(config)) + + +def _default_config() -> dict[str, Any]: + return { + "default_image": { + "codec": CODEC_JPEG2K, + "preset": "lossless", + "chunks": "auto", + }, + "images": {}, + "default_labels": { + "codec": "blosc", + "clevel": 5, + }, + "labels": {}, + } + + +def _deep_merge(base: dict[str, Any], override: dict[str, Any]) -> dict[str, Any]: + out = dict(base) + for key, value in override.items(): + if isinstance(value, dict) and isinstance(out.get(key), dict): + out[key] = _deep_merge(out[key], value) + else: + out[key] = value + return out + + +def _apply_image_shortcuts( + image_cfg: dict[str, Any], + *, + codec: str | None = None, + preset: ImagePreset | None = None, + chunks: ChunkSpec | None = None, + quality: float | None = None, + reversible: bool | None = None, +) -> dict[str, Any]: + out = dict(image_cfg) + if codec is not None: + out["codec"] = codec + if preset is not None: + out["preset"] = preset + if chunks is not None: + out["chunks"] = chunks + if quality is not None: + out["quality"] = quality + if reversible is not None: + out["reversible"] = reversible + return out + + +def resolve_recompression_config( + config: str | Path | dict[str, Any] | None = None, + *, + image_key: str | None = None, + codec: str | None = None, + preset: ImagePreset | None = None, + chunks: ChunkSpec | None = None, + quality: float | None = None, + reversible: bool | None = None, +) -> dict[str, Any]: + """Return normalized recompression config after CLI shortcut expansion. + + When *image_key* is set, shortcut flags apply to that image only. Otherwise + they update ``default_image`` and apply to every image in the store. + """ + + resolved = _deep_merge(_default_config(), _load_config(config)) + shortcuts = _apply_image_shortcuts( + {}, + codec=codec, + preset=preset, + chunks=chunks, + quality=quality, + reversible=reversible, + ) + if image_key is not None: + image_cfg = _apply_image_shortcuts( + dict(resolved.get("images", {}).get(image_key, {})), + codec=codec, + preset=preset, + chunks=chunks, + quality=quality, + reversible=reversible, + ) + resolved.setdefault("images", {})[image_key] = image_cfg + elif shortcuts: + resolved["default_image"] = _deep_merge(resolved.get("default_image", {}), shortcuts) + return resolved + + +def _list_raster_keys(store_path: Path, kind: Literal["images", "labels"]) -> list[str]: + root = store_path / kind + if not root.exists(): + return [] + return sorted(path.name for path in root.iterdir() if path.is_dir()) + + +def _attrs_from_node(path: Path) -> dict[str, Any]: + meta_path = path / "zarr.json" + if not meta_path.exists(): + return {} + return _read_json(meta_path).get("attributes", {}) + + +def _datasets_from_raster_group(path: Path) -> list[str]: + attrs = _attrs_from_node(path) + ome_attrs = attrs.get("ome", attrs) + if isinstance(ome_attrs, dict): + multiscales = ome_attrs.get("multiscales") + datasets = multiscales[0].get("datasets") if multiscales else None + if datasets: + return [str(dataset["path"]) for dataset in datasets if "path" in dataset] + + levels = [] + for child in path.iterdir() if path.exists() else []: + if child.is_dir() and (child / "zarr.json").exists(): + meta = _read_json(child / "zarr.json") + if meta.get("node_type") == "array": + levels.append(child.name) + return sorted(levels, key=lambda value: (not value.isdigit(), value)) + + +def _auto_image_chunks(shape: tuple[int, ...], max_spatial: int = 1024) -> tuple[int, ...]: + if len(shape) < 2: + raise ValueError(f"Expected at least 2D raster shape, got {shape}") + return (*([1] * (len(shape) - 2)), min(max_spatial, shape[-2]), min(max_spatial, shape[-1])) + + +def _normalize_chunks(spec: ChunkSpec, shape: tuple[int, ...], *, image: bool) -> tuple[int, ...]: + if spec == "auto": + return _auto_image_chunks(shape) if image else tuple(min(size, 1024) for size in shape) + chunks = tuple(int(value) for value in spec) + if len(chunks) != len(shape): + raise ValueError(f"Chunk spec {chunks} does not match raster shape {shape}") + return chunks + + +def _validate_browser_image_codec_dtype(dtype: np.dtype, raster_path: str) -> None: + if dtype not in SUPPORTED_BROWSER_JP2K_DTYPES: + supported = ", ".join( + str(dtype) for dtype in sorted(SUPPORTED_BROWSER_JP2K_DTYPES, key=str) + ) + raise TypeError( + f"Browser image codecs support only <=16-bit integer dtypes ({supported}); " + f"{raster_path} has dtype {dtype}. Use Blosc for labels or skip this raster." + ) + + +def _validate_browser_image_codec_chunks(chunks: tuple[int, ...], raster_path: str) -> None: + if len(chunks) < 2: + raise ValueError(f"{raster_path} must be at least 2D") + non_spatial = chunks[:-2] + if any(chunk != 1 for chunk in non_spatial): + raise ValueError( + f"{raster_path} image codec chunks must have singleton non-spatial axes; got {chunks}." + ) + + +def _resolve_image_codec(config: dict[str, Any], raster_key: str) -> str: + codec = config.get("codec", CODEC_JPEG2K) + if codec not in SUPPORTED_IMAGE_CODECS: + supported = ", ".join(sorted(SUPPORTED_IMAGE_CODECS)) + raise ValueError( + f"Unsupported image codec for {raster_key!r}: {codec!r}; expected one of {supported}" + ) + if codec == CODEC_HTJ2K_OPENJPH and not htj2k_encode_available(): + raise RuntimeError( + f"HTJ2K recompression requested for {raster_key!r}, but the OpenJPH WASM encoder " + "is not available. Install spatialdata-codec-writer and ensure Node.js is on PATH." + ) + return codec + + +def _array_metadata_from_source( + source_meta: dict[str, Any], + *, + chunks: tuple[int, ...], + codecs: list[dict[str, Any]], +) -> dict[str, Any]: + meta = dict(source_meta) + meta["chunk_grid"] = { + "name": "regular", + "configuration": {"chunk_shape": list(chunks)}, + } + meta["chunk_key_encoding"] = { + "name": "default", + "configuration": {"separator": "/"}, + } + meta["codecs"] = codecs + return meta + + +def _preset_encode_options(config: dict[str, Any], *, codec: str) -> dict[str, Any]: + presets = HTJ2K_PRESETS if codec == CODEC_HTJ2K_OPENJPH else JP2K_PRESETS + preset_family = "HTJ2K" if codec == CODEC_HTJ2K_OPENJPH else "JP2K" + encode_options = dict(config.get("encode_options", {})) + + preset = config.get("preset") + has_explicit_quality = "quality" in config or "quality" in encode_options + if preset is not None: + if preset not in presets: + raise ValueError( + f"Unknown {preset_family} preset {preset!r}; expected one of {sorted(presets)}" + ) + options = dict(presets[preset]) + elif has_explicit_quality and codec == CODEC_HTJ2K_OPENJPH: + options = {} + else: + options = dict(presets["lossless"]) + + options.update(encode_options) + for key in ("level", "quality", "reversible", "codecformat", "numthreads"): + if key in config: + options[key] = config[key] + + explicit_lossless = config.get("reversible") is True or encode_options.get("reversible") is True + if options.get("quality") is not None and not explicit_lossless: + options["reversible"] = False + + return options + + +def _sibling_image_label(image_config: dict[str, Any]) -> str: + """Return a sibling suffix label from preset and/or explicit encode settings.""" + encode_options = image_config.get("encode_options", {}) + quality = image_config.get("quality", encode_options.get("quality")) + if quality is not None and image_config.get("reversible") is not True: + return f"q{float(quality):g}" + preset = image_config.get("preset", "lossless") + return str(preset) + + +def _sample_values(plane: np.ndarray) -> list[int | float]: + values = [ + plane[0, 0], + plane[0, min(1, plane.shape[1] - 1)], + plane[min(1, plane.shape[0] - 1), 0], + ] + return [value.item() if hasattr(value, "item") else value for value in values] + + +def _encode_chunk_task( + plane: np.ndarray, codec: str, encode_options: dict[str, Any] +) -> bytes | bytearray: + return encode_image_plane(plane, codec, encode_options) + + +def _chunk_plane( + source_array: Any, shape: tuple[int, ...], chunks: tuple[int, ...], coords: tuple[int, ...] +) -> np.ndarray: + selection = chunk_slices(shape, chunks, coords) + chunk = pad_chunk(np.asarray(source_array[selection]), chunks) + return chunk.reshape(chunk.shape[-2], chunk.shape[-1]) + + +def _write_encoded_chunk( + dest_array_path: Path, coords: tuple[int, ...], encoded: bytes | bytearray +) -> None: + chunk_rel = Path("c").joinpath(*(str(coord) for coord in coords)) + chunk_path = dest_array_path / chunk_rel + chunk_path.parent.mkdir(parents=True, exist_ok=True) + chunk_path.write_bytes(encoded) + + +def _maybe_record_chunk_check( + *, + chunks_checked: list[dict[str, Any]], + coords: tuple[int, ...], + encoded: bytes | bytearray, + plane: np.ndarray, + codec: str, + raster_path: str, + is_lossless: bool, +) -> None: + if len(chunks_checked) >= 4: + return + decoded = decode_image_plane(encoded, codec) + decoded_plane = decoded.reshape(plane.shape) + if is_lossless and not np.array_equal(decoded_plane, plane): + raise RuntimeError( + f"Lossless {codec} self-validation failed for {raster_path} chunk {coords}" + ) + chunks_checked.append( + { + "coords": list(coords), + "encoded_sha256": sha256(encoded), + "decoded_sha256": sha256(decoded_plane.tobytes()), + "source_sha256": sha256(plane.tobytes()), + "samples": _sample_values(decoded_plane), + } + ) + + +def _recompress_image_array( + *, + source_array_path: Path, + dest_array_path: Path, + raster_path: str, + config: dict[str, Any], + workers: int, +) -> dict[str, Any]: + source_meta = _read_json(source_array_path / "zarr.json") + source_array = zarr.open_array(str(source_array_path), mode="r") + shape = tuple(int(value) for value in source_array.shape) + dtype = np.dtype(source_array.dtype) + codec = _resolve_image_codec(config, raster_path) + _validate_browser_image_codec_dtype(dtype, raster_path) + + chunks = _normalize_chunks(config.get("chunks", "auto"), shape, image=True) + _validate_browser_image_codec_chunks(chunks, raster_path) + encode_options = _preset_encode_options(config, codec=codec) + is_lossless = bool(encode_options.get("reversible", False)) + + if dest_array_path.exists(): + shutil.rmtree(dest_array_path) + (dest_array_path / "c").mkdir(parents=True) + write_json( + dest_array_path / "zarr.json", + _array_metadata_from_source( + source_meta, + chunks=chunks, + codecs=[{"name": codec, "configuration": {}}], + ), + ) + + chunk_coords_list = list(chunk_grid(shape, chunks)) + chunks_checked: list[dict[str, Any]] = [] + encoded_bytes = 0 + chunk_count = 0 + + if workers <= 1 or len(chunk_coords_list) <= 1: + for coords in chunk_coords_list: + plane = _chunk_plane(source_array, shape, chunks, coords) + encoded = _encode_chunk_task(plane, codec, encode_options) + encoded_bytes += len(encoded) + chunk_count += 1 + _write_encoded_chunk(dest_array_path, coords, encoded) + _maybe_record_chunk_check( + chunks_checked=chunks_checked, + coords=coords, + encoded=encoded, + plane=plane, + codec=codec, + raster_path=raster_path, + is_lossless=is_lossless, + ) + else: + with ThreadPoolExecutor(max_workers=workers) as executor: + future_to_job = { + executor.submit(_encode_chunk_task, plane, codec, encode_options): (coords, plane) + for coords in chunk_coords_list + for plane in [_chunk_plane(source_array, shape, chunks, coords)] + } + for future in as_completed(future_to_job): + coords, plane = future_to_job[future] + encoded = future.result() + encoded_bytes += len(encoded) + chunk_count += 1 + _write_encoded_chunk(dest_array_path, coords, encoded) + _maybe_record_chunk_check( + chunks_checked=chunks_checked, + coords=coords, + encoded=encoded, + plane=plane, + codec=codec, + raster_path=raster_path, + is_lossless=is_lossless, + ) + + report: dict[str, Any] = { + "path": raster_path, + "codec": codec, + "preset": config.get("preset", "lossless"), + "encode_options": encode_options, + "shape": list(shape), + "dtype": str(dtype), + "chunks": list(chunks), + "chunk_count": chunk_count, + "encoded_bytes": encoded_bytes, + "lossless": is_lossless, + "chunks_checked": chunks_checked, + } + if is_htj2k_codec(codec): + report["encoder"] = HTJ2K_ENCODER + return report + + +def _blosc_codec(dtype: np.dtype, clevel: int) -> BloscCodec: + if dtype.kind not in ("u", "i"): + raise TypeError(f"Labels must be integer dtype for Blosc label compression, got {dtype}") + return BloscCodec( + cname="zstd", + clevel=clevel, + shuffle=BloscShuffle.shuffle, + typesize=max(1, dtype.itemsize), + ) + + +def _recompress_label_array( + *, + source_array_path: Path, + dest_array_path: Path, + raster_path: str, + config: dict[str, Any], +) -> dict[str, Any]: + source_meta = _read_json(source_array_path / "zarr.json") + source_array = zarr.open_array(str(source_array_path), mode="r") + shape = tuple(int(value) for value in source_array.shape) + dtype = np.dtype(source_array.dtype) + chunks = _normalize_chunks(config.get("chunks", source_array.chunks), shape, image=False) + codec = _blosc_codec(dtype, int(config.get("clevel", 5))) + + if dest_array_path.exists(): + shutil.rmtree(dest_array_path) + dest_array_path.mkdir(parents=True) + dest_array = zarr.create_array( + store=str(dest_array_path), + shape=shape, + chunks=chunks, + dtype=dtype, + compressors=[codec], + fill_value=source_meta.get("fill_value", 0), + attributes=source_meta.get("attributes", {}), + dimension_names=source_meta.get("dimension_names"), + zarr_format=3, + overwrite=True, + ) + + chunk_count = 0 + for coords in chunk_grid(shape, chunks): + selection = chunk_slices(shape, chunks, coords) + dest_array[selection] = source_array[selection] + chunk_count += 1 + + meta = _read_json(dest_array_path / "zarr.json") + return { + "path": raster_path, + "codec": "blosc", + "shape": list(shape), + "dtype": str(dtype), + "chunks": list(chunks), + "chunk_count": chunk_count, + "codecs": meta.get("codecs", []), + } + + +def _collect_consolidated_metadata(store_path: Path) -> dict[str, Any]: + metadata: dict[str, Any] = {} + for meta_path in store_path.rglob("zarr.json"): + if meta_path == store_path / "zarr.json": + continue + rel = meta_path.parent.relative_to(store_path).as_posix() + metadata[rel] = _read_json(meta_path) + return metadata + + +def _refresh_consolidated_metadata(store_path: Path) -> None: + root_path = store_path / "zarr.json" + root_meta = _read_json(root_path) + root_meta["consolidated_metadata"] = { + "kind": "inline", + "must_understand": False, + "metadata": _collect_consolidated_metadata(store_path), + } + write_json(root_path, root_meta) + + +def _prepare_path_source(source_path: Path, dest: Path, *, overwrite: bool) -> Path: + if dest.exists(): + if not overwrite: + raise FileExistsError(dest) + shutil.rmtree(dest) + + shutil.copytree(source_path, dest) + return source_path + + +def _codec_sibling_suffix(codec: str) -> str: + if is_htj2k_codec(codec): + return "htj2k" + return "jp2k" + + +def _sibling_image_key(key: str, codec: str, preset: str) -> str: + """Return the sibling image key, e.g. ``morphology:jp2k_lossless``.""" + return f"{key}:{_codec_sibling_suffix(codec)}_{preset}" + + +def recompress_spatialdata( + source: str | Path | Any, + dest: str | Path, + *, + config: str | Path | dict[str, Any] | None = None, + overwrite: bool = False, + manifest: bool = True, + image_key: str | None = None, + codec: str | None = None, + preset: ImagePreset | None = None, + chunks: ChunkSpec | None = None, + quality: float | None = None, + reversible: bool | None = None, + sibling: bool = False, + workers: int | None = None, +) -> RecompressedSpatialData: + """Preserve a SpatialData store and recompress configured rasters. + + When *sibling* is ``False`` (default) each configured image is rewritten + in-place with the new codec. When *sibling* is ``True`` the original + image is kept and a new image group is added alongside it whose name is + ``{original_key}:{codec}_{preset}`` (e.g. ``morphology_focus:jp2k_lossless`` + or ``morphology_focus:htj2k_balanced``). This lets the original remain + available for tools that lack the target codec while the compressed version + is used where it is supported. + + Path sources are copied before raster replacement, which keeps tables, + shapes, points, and unconfigured rasters intact without loading the whole + object. + """ + + import os + + worker_count = workers if workers is not None else (os.cpu_count() or 1) + configure_encoder_pool(worker_count) + + dest_path = Path(dest) + temp_dir: tempfile.TemporaryDirectory[str] | None = None + try: + if isinstance(source, str | Path): + read_path = _prepare_path_source(Path(source), dest_path, overwrite=overwrite) + source_label = str(source) + else: + if dest_path.exists(): + if not overwrite: + raise FileExistsError(dest_path) + shutil.rmtree(dest_path) + temp_dir = tempfile.TemporaryDirectory(prefix="spatialdata-codec-writer-") + read_path = Path(temp_dir.name) / "source.zarr" + source.write(str(read_path), overwrite=True) + shutil.copytree(read_path, dest_path) + source_label = None + + resolved_config = resolve_recompression_config( + config, + image_key=image_key, + codec=codec, + preset=preset, + chunks=chunks, + quality=quality, + reversible=reversible, + ) + + image_keys = list(resolved_config.get("images") or {}) + if not image_keys: + image_keys = _list_raster_keys(dest_path, "images") + + label_keys = list(resolved_config.get("labels") or {}) + if not label_keys and resolved_config.get("default_labels", {}).get("codec") == "blosc": + label_keys = _list_raster_keys(dest_path, "labels") + + image_reports = [] + default_image = resolved_config.get("default_image", {}) + for key in image_keys: + image_config = _deep_merge(default_image, resolved_config.get("images", {}).get(key, {})) + resolved_codec = _resolve_image_codec(image_config, key) + + if sibling: + dest_key = _sibling_image_key( + key, + resolved_codec, + _sibling_image_label(image_config), + ) + sib_group_path = dest_path / "images" / dest_key + if sib_group_path.exists(): + shutil.rmtree(sib_group_path) + sib_group_path.mkdir(parents=True) + src_group_meta = read_path / "images" / key / "zarr.json" + if src_group_meta.exists(): + shutil.copy2(src_group_meta, sib_group_path / "zarr.json") + else: + dest_key = key + + for dataset in _datasets_from_raster_group( + dest_path / "images" / key if not sibling else read_path / "images" / key + ): + source_raster = f"images/{key}/{dataset}" + dest_raster = f"images/{dest_key}/{dataset}" + image_reports.append( + _recompress_image_array( + source_array_path=read_path / source_raster, + dest_array_path=dest_path / dest_raster, + raster_path=dest_raster, + config=image_config, + workers=worker_count, + ) + ) + + label_reports = [] + default_label = resolved_config.get("default_labels", {}) + if default_label.get("codec", "blosc") not in {"blosc", None}: + raise ValueError(f"Unsupported label codec: {default_label.get('codec')!r}") + for key in label_keys: + label_config = _deep_merge(default_label, resolved_config.get("labels", {}).get(key, {})) + if label_config.get("codec", "blosc") != "blosc": + raise ValueError( + f"Labels only support Blosc compression in v1, got {label_config.get('codec')!r}" + ) + for dataset in _datasets_from_raster_group(dest_path / "labels" / key): + raster_path = f"labels/{key}/{dataset}" + label_reports.append( + _recompress_label_array( + source_array_path=read_path / raster_path, + dest_array_path=dest_path / raster_path, + raster_path=raster_path, + config=label_config, + ) + ) + + _refresh_consolidated_metadata(dest_path) + + manifest_data = { + "format": "spatialdata-codec-recompression/v1", + "source": source_label, + "output": str(dest_path), + "config": resolved_config, + "images": image_reports, + "labels": label_reports, + "workers": worker_count, + "packages": { + "imagecodecs": package_version("imagecodecs"), + "numpy": package_version("numpy"), + "spatialdata": package_version("spatialdata"), + "zarr": package_version("zarr"), + }, + } + manifest_path = dest_path.with_suffix(".manifest.json") if manifest else None + if manifest_path is not None: + write_json(manifest_path, manifest_data) + return RecompressedSpatialData(dest_path, manifest_path, manifest_data) + finally: + if temp_dir is not None: + temp_dir.cleanup() diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/synthetic_cli.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/synthetic_cli.py new file mode 100644 index 00000000..c294b16e --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/synthetic_cli.py @@ -0,0 +1,17 @@ +"""Console entry for repo-local synthetic image writer scripts.""" + +from __future__ import annotations + +import sys +from pathlib import Path + + +def main(argv: list[str] | None = None) -> None: + scripts_dir = Path(__file__).resolve().parents[2] / "scripts" + scripts_path = str(scripts_dir) + if scripts_path not in sys.path: + sys.path.insert(0, scripts_path) + + from write_synthetic import main as write_synthetic_main + + write_synthetic_main(argv) diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/__init__.py b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/__init__.py new file mode 100644 index 00000000..d899a861 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/__init__.py @@ -0,0 +1 @@ +"""Vendored OpenJPH WASM assets and Node encode driver.""" diff --git a/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/encode-plane.mjs b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/encode-plane.mjs new file mode 100644 index 00000000..15764bd0 --- /dev/null +++ b/python/spatialdata-codec-writer/src/spatialdata_codec_writer/vendor/encode-plane.mjs @@ -0,0 +1,156 @@ +#!/usr/bin/env node +/** + * Encode one 2D image plane to HTJ2K via vendored OpenJPH WASM. + * + * One-shot mode (default): + * stdin: JSON { width, height, dtype, reversible?, quality?, plane: base64 } + * stdout: raw HTJ2K bytes + * + * Worker mode (--worker): + * Repeated length-prefixed requests on stdin; length-prefixed responses on stdout. + * Request: [u32 BE length][JSON utf8] + * Response: [u8 status][u32 BE length][payload] + * status 0 = HTJ2K bytes + * status 1 = UTF-8 error message + */ +import { fileURLToPath, pathToFileURL } from 'node:url'; +import { dirname, join } from 'node:path'; + +const vendorDir = dirname(fileURLToPath(import.meta.url)); +const openjphDir = join(vendorDir, 'openjph'); +const workerMode = process.argv.includes('--worker'); + +async function readStdin() { + const chunks = []; + for await (const chunk of process.stdin) { + chunks.push(chunk); + } + return Buffer.concat(chunks); +} + +function planeArrayForDtype(dtype, bytes) { + switch (dtype) { + case 'uint8': + return new Uint8Array(bytes.buffer, bytes.byteOffset, bytes.byteLength); + case 'int8': + return new Int8Array(bytes.buffer, bytes.byteOffset, bytes.byteLength); + case 'uint16': + return new Uint16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + case 'int16': + return new Int16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + default: + throw new Error(`Unsupported plane dtype '${dtype}'.`); + } +} + +async function loadEncoder() { + const mod = await import(pathToFileURL(join(openjphDir, 'openjphjs.js')).href); + const factory = mod.default ?? mod.OpenJPHJS ?? mod; + if (typeof factory !== 'function') { + throw new Error('Could not load OpenJPH WASM factory.'); + } + const wasmPath = join(openjphDir, 'openjphjs.wasm'); + return await factory({ + locateFile: (path) => (path.endsWith('.wasm') ? wasmPath : path), + }); +} + +async function encodePlane(runtime, request) { + const Encoder = runtime.HTJ2KEncoder; + if (!Encoder) { + throw new Error('OpenJPH runtime does not expose HTJ2KEncoder.'); + } + + const { width, height, dtype } = request; + const reversible = request.reversible ?? true; + const quality = request.quality ?? 0; + const planeBytes = Buffer.from(request.plane, 'base64'); + const plane = planeArrayForDtype(dtype, planeBytes); + const expectedValues = width * height; + if (plane.length !== expectedValues) { + throw new Error(`Plane has ${plane.length} samples, expected ${expectedValues}.`); + } + + const frame = { + width, + height, + bitsPerSample: dtype === 'uint8' || dtype === 'int8' ? 8 : 16, + isSigned: dtype === 'int8' || dtype === 'int16', + componentCount: 1, + isUsingColorTransform: false, + }; + + const encoder = new Encoder(); + encoder.setQuality(reversible, quality); + const buffer = encoder.getDecodedBuffer(frame); + const target = + frame.bitsPerSample === 16 + ? new Uint16Array(buffer.buffer, buffer.byteOffset, plane.length) + : new Uint8Array(buffer.buffer, buffer.byteOffset, plane.length); + target.set(plane); + encoder.encode(); + return encoder.getEncodedBuffer(); +} + +function writeResponse(status, payload) { + const header = Buffer.alloc(5); + header.writeUInt8(status, 0); + header.writeUInt32BE(payload.length, 1); + process.stdout.write(header); + if (payload.length > 0) { + process.stdout.write(payload); + } +} + +async function* readLengthPrefixedJson(stream) { + let buffer = Buffer.alloc(0); + for await (const chunk of stream) { + buffer = Buffer.concat([buffer, chunk]); + while (buffer.length >= 4) { + const length = buffer.readUInt32BE(0); + if (buffer.length < 4 + length) { + break; + } + const body = buffer.subarray(4, 4 + length); + buffer = buffer.subarray(4 + length); + yield JSON.parse(body.toString('utf8')); + } + } +} + +async function runWorker(runtime) { + for await (const request of readLengthPrefixedJson(process.stdin)) { + try { + const encoded = await encodePlane(runtime, request); + writeResponse(0, Buffer.from(encoded)); + } catch (error) { + const message = error instanceof Error ? error.message : String(error); + writeResponse(1, Buffer.from(message, 'utf8')); + } + } +} + +async function runOnce(runtime) { + const request = JSON.parse((await readStdin()).toString('utf8')); + const encoded = await encodePlane(runtime, request); + process.stdout.write(Buffer.from(encoded)); +} + +async function main() { + const runtime = await loadEncoder(); + if (workerMode) { + await runWorker(runtime); + return; + } + await runOnce(runtime); +} + +main().catch((error) => { + const message = error instanceof Error ? error.message : String(error); + if (workerMode) { + writeResponse(1, Buffer.from(message, 'utf8')); + process.exit(1); + } + process.stderr.write(`${message}\n`); + process.exit(1); +}); diff --git a/python/spatialdata-codec-writer/tests/conftest.py b/python/spatialdata-codec-writer/tests/conftest.py new file mode 100644 index 00000000..ed481e2e --- /dev/null +++ b/python/spatialdata-codec-writer/tests/conftest.py @@ -0,0 +1,8 @@ +from __future__ import annotations + +import sys +from pathlib import Path + +_SCRIPTS_DIR = Path(__file__).resolve().parent.parent / "scripts" +if str(_SCRIPTS_DIR) not in sys.path: + sys.path.insert(0, str(_SCRIPTS_DIR)) diff --git a/python/spatialdata-codec-writer/tests/test_htj2k_encode.py b/python/spatialdata-codec-writer/tests/test_htj2k_encode.py new file mode 100644 index 00000000..0a98db26 --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_htj2k_encode.py @@ -0,0 +1,51 @@ +from __future__ import annotations + +import numpy as np +import pytest + +from spatialdata_codec_writer.htj2k_encode import ( + EncoderPool, + encode_htj2k_plane, + encode_script_path, + htj2k_encode_available, + openjph_vendor_dir, + shutdown_encoder_pool, +) + + +def test_vendored_encode_assets_exist() -> None: + assert encode_script_path().is_file() + assert (openjph_vendor_dir() / "openjphjs.js").is_file() + assert (openjph_vendor_dir() / "openjphjs.wasm").is_file() + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_encoder_pool_round_trip() -> None: + shutdown_encoder_pool() + pool = EncoderPool(workers=2) + try: + plane = np.arange(16, dtype=np.uint16).reshape(4, 4) + encoded_a = pool.encode_plane(plane, reversible=True, quality=0.0) + encoded_b = pool.encode_plane(plane, reversible=True, quality=0.0) + assert len(encoded_a) > 0 + assert len(encoded_b) > 0 + finally: + pool.close() + shutdown_encoder_pool() + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_encode_htj2k_plane_uses_global_pool() -> None: + shutdown_encoder_pool() + try: + plane = np.zeros((8, 8), dtype=np.uint16) + encoded = encode_htj2k_plane(plane, reversible=True, quality=0.0) + assert len(encoded) > 0 + finally: + shutdown_encoder_pool() diff --git a/python/spatialdata-codec-writer/tests/test_htj2k_encode_demo.py b/python/spatialdata-codec-writer/tests/test_htj2k_encode_demo.py new file mode 100644 index 00000000..1b47dc29 --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_htj2k_encode_demo.py @@ -0,0 +1,37 @@ +from pathlib import Path + +import pytest + +from spatialdata_codec_writer import htj2k_encode_available + +from htj2k_fixtures import HTJ2K_ENCODE_DEMO_STORE, htj2k_encode_demo_image_key, write_htj2k_encode_demo_fixtures + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_htj2k_encode_demo_fixtures(tmp_path: Path) -> None: + manifest_path = write_htj2k_encode_demo_fixtures(tmp_path, overwrite=True) + manifest = manifest_path.read_text() + + assert "spatialdata-htj2k-encode-demo/v2" in manifest + store_path = tmp_path / HTJ2K_ENCODE_DEMO_STORE + assert store_path.is_dir() + assert (store_path / "images" / htj2k_encode_demo_image_key("lossless")).is_dir() + assert (store_path / "images" / htj2k_encode_demo_image_key("balanced")).is_dir() + assert (store_path / "images" / htj2k_encode_demo_image_key("small")).is_dir() + + import json + + parsed = json.loads(manifest) + assert parsed["store"] == HTJ2K_ENCODE_DEMO_STORE + assert parsed["image"]["shape"] == [1, 1, 1, 512, 512] + assert len(parsed["variants"]) == 3 + + lossless = next(v for v in parsed["variants"] if v["suffix"] == "lossless") + small = next(v for v in parsed["variants"] if v["suffix"] == "small") + assert lossless["image_key"] == htj2k_encode_demo_image_key("lossless") + assert lossless["lossless"] is True + assert small["lossless"] is False + assert small["encoded_bytes"] < lossless["encoded_bytes"] diff --git a/python/spatialdata-codec-writer/tests/test_htj2k_quality.py b/python/spatialdata-codec-writer/tests/test_htj2k_quality.py new file mode 100644 index 00000000..c65e7845 --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_htj2k_quality.py @@ -0,0 +1,37 @@ +from __future__ import annotations + +import json +from pathlib import Path + +import pytest + +from spatialdata_codec_writer import htj2k_encode_available + +from htj2k_fixtures import write_htj2k_quality_sweep_manifest + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="OpenJPH WASM HTJ2K encoder is not available in this environment.", +) +def test_htj2k_quality_sweep_responds_to_quantization(tmp_path: Path) -> None: + manifest_path = write_htj2k_quality_sweep_manifest( + tmp_path / "htj2k-quality-sweep.manifest.json" + ) + manifest = json.loads(manifest_path.read_text()) + + assert manifest["format"] == "spatialdata-htj2k-quality-sweep/v1" + assert manifest["encoder"] == "openjph-wasm" + assert manifest["image"]["kind"] == "mandelbrot" + + by_label = {entry["label"]: entry for entry in manifest["qualities"]} + lossless = by_label["lossless"] + high = by_label["q0.001"] + mid = by_label["q0.01"] + low = by_label["q0.1"] + + assert lossless["rmse"] == 0.0 + assert lossless["encoded_bytes"] > high["encoded_bytes"] + assert high["encoded_bytes"] > mid["encoded_bytes"] + assert mid["encoded_bytes"] > low["encoded_bytes"] + assert high["rmse"] < mid["rmse"] < low["rmse"] diff --git a/python/spatialdata-codec-writer/tests/test_recompress.py b/python/spatialdata-codec-writer/tests/test_recompress.py new file mode 100644 index 00000000..dca0b999 --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_recompress.py @@ -0,0 +1,476 @@ +from __future__ import annotations + +import json +from pathlib import Path + +import imagecodecs +import numpy as np +import pytest +import zarr + +from spatialdata_codec_writer import ( + CODEC_HTJ2K_OPENJPH, + CODEC_JPEG2K, + HTJ2K_PRESETS, + JP2K_PRESETS, + htj2k_encode_available, + recompress_spatialdata, + resolve_recompression_config, +) +from spatialdata_codec_writer.codecs import decode_htj2k_plane, encode_image_plane +from spatialdata_codec_writer.recompress import _preset_encode_options + +from synthetic_images import mandelbrot_plane + + +def _write_json(path: Path, value: dict) -> None: + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(json.dumps(value, indent=2, sort_keys=True)) + + +def _group_meta(attributes: dict | None = None) -> dict: + return {"zarr_format": 3, "node_type": "group", "attributes": attributes or {}} + + +def _raster_attrs(name: str, axes: list[str]) -> dict: + return { + "ome": { + "multiscales": [ + { + "name": name, + "axes": [{"name": axis} for axis in axes], + "datasets": [{"path": "0"}], + } + ] + } + } + + +def _write_source_store(root: Path, *, image_dtype: str = "uint16") -> Path: + _write_json(root / "zarr.json", _group_meta({"spatialdata_attrs": {"version": "0.7.2"}})) + _write_json(root / "images" / "zarr.json", _group_meta()) + _write_json( + root / "images" / "morphology" / "zarr.json", + _group_meta(_raster_attrs("morphology", ["c", "y", "x"])), + ) + _write_json(root / "labels" / "zarr.json", _group_meta()) + _write_json( + root / "labels" / "cells" / "zarr.json", + _group_meta(_raster_attrs("cells", ["y", "x"])), + ) + _write_json(root / "tables" / "table" / "zarr.json", _group_meta({"kept": True})) + + image = zarr.create_array( + store=str(root / "images" / "morphology" / "0"), + shape=(1, 8, 8), + chunks=(1, 4, 4), + dtype=image_dtype, + dimension_names=("c", "y", "x"), + zarr_format=3, + ) + image[:] = np.arange(64, dtype=np.dtype(image_dtype)).reshape(1, 8, 8) + + labels = zarr.create_array( + store=str(root / "labels" / "cells" / "0"), + shape=(8, 8), + chunks=(4, 4), + dtype="uint32", + dimension_names=("y", "x"), + zarr_format=3, + ) + labels[:] = np.arange(64, dtype=np.uint32).reshape(8, 8) + return root + + +def test_resolve_recompression_config_applies_cli_shortcuts() -> None: + config = resolve_recompression_config( + {"default_image": {"preset": "lossless"}}, + image_key="morphology", + preset="balanced", + chunks=(1, 4, 4), + ) + + assert config["images"]["morphology"]["preset"] == "balanced" + assert config["images"]["morphology"]["chunks"] == (1, 4, 4) + assert config["default_image"]["preset"] == "lossless" + + +def test_resolve_recompression_config_applies_codec_shortcut() -> None: + config = resolve_recompression_config( + {}, + image_key="morphology", + codec=CODEC_HTJ2K_OPENJPH, + preset="lossless", + ) + + assert config["images"]["morphology"]["codec"] == CODEC_HTJ2K_OPENJPH + assert config["images"]["morphology"]["preset"] == "lossless" + assert config["default_image"]["codec"] == "imagecodecs_jpeg2k" + + +def test_resolve_recompression_config_applies_quality_shortcut() -> None: + config = resolve_recompression_config( + {}, + image_key="morphology", + codec=CODEC_HTJ2K_OPENJPH, + quality=0.001, + ) + + assert config["images"]["morphology"]["quality"] == 0.001 + assert "preset" not in config["images"]["morphology"] + + +def test_resolve_recompression_config_applies_shortcuts_to_all_images() -> None: + config = resolve_recompression_config( + {}, + codec=CODEC_HTJ2K_OPENJPH, + quality=0.0005, + chunks="auto", + ) + + assert config["images"] == {} + assert config["default_image"]["codec"] == CODEC_HTJ2K_OPENJPH + assert config["default_image"]["quality"] == 0.0005 + assert config["default_image"]["chunks"] == "auto" + + +def _write_multi_image_store(root: Path) -> Path: + store = _write_source_store(root) + _write_json( + root / "images" / "histology" / "zarr.json", + _group_meta(_raster_attrs("histology", ["c", "y", "x"])), + ) + image = zarr.create_array( + store=str(root / "images" / "histology" / "0"), + shape=(1, 8, 8), + chunks=(1, 4, 4), + dtype="uint16", + dimension_names=("c", "y", "x"), + zarr_format=3, + ) + image[:] = (np.arange(64, dtype=np.uint16) * 2).reshape(1, 8, 8) + return store + + +def test_recompress_spatialdata_applies_default_image_to_all_images(tmp_path: Path) -> None: + source = _write_multi_image_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + preset="lossless", + chunks=[1, 4, 4], + config={"default_labels": {"codec": None}}, + ) + + assert {report["path"] for report in result.manifest["images"]} == { + "images/morphology/0", + "images/histology/0", + } + for image_key in ("morphology", "histology"): + image_meta = json.loads( + (result.store_path / "images" / image_key / "0" / "zarr.json").read_text() + ) + assert image_meta["codecs"] == [{"name": "imagecodecs_jpeg2k", "configuration": {}}] + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_recompress_sibling_applies_to_all_images(tmp_path: Path) -> None: + source = _write_multi_image_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + codec=CODEC_HTJ2K_OPENJPH, + quality=0.0005, + chunks=[1, 4, 4], + config={"default_labels": {"codec": None}}, + sibling=True, + ) + + assert {report["path"] for report in result.manifest["images"]} == { + "images/morphology:htj2k_q0.0005/0", + "images/histology:htj2k_q0.0005/0", + } + for image_key in ("morphology", "histology"): + original_meta = json.loads( + (result.store_path / "images" / image_key / "0" / "zarr.json").read_text() + ) + assert original_meta["codecs"] != [ + {"name": CODEC_HTJ2K_OPENJPH, "configuration": {}} + ] + + sibling_meta = json.loads( + ( + result.store_path + / "images" + / f"{image_key}:htj2k_q0.0005" + / "0" + / "zarr.json" + ).read_text() + ) + assert sibling_meta["codecs"] == [ + {"name": CODEC_HTJ2K_OPENJPH, "configuration": {}} + ] + + +def test_preset_encode_options_quality_implies_lossy_htj2k() -> None: + assert _preset_encode_options( + {"quality": 0.001}, + codec=CODEC_HTJ2K_OPENJPH, + ) == {"reversible": False, "quality": 0.001} + assert _preset_encode_options( + {"preset": "lossless", "quality": 0.001}, + codec=CODEC_HTJ2K_OPENJPH, + ) == {"reversible": False, "quality": 0.001} + + +def test_lossy_presets_are_not_extreme_low_bitrate() -> None: + assert JP2K_PRESETS["balanced"] == {"reversible": False, "level": 100} + assert JP2K_PRESETS["small"] == {"reversible": False, "level": 75} + + +def test_htj2k_presets_do_not_pass_jp2k_rate_control_levels() -> None: + assert HTJ2K_PRESETS["balanced"] == {"reversible": False, "quality": 0.0002} + assert HTJ2K_PRESETS["small"] == {"reversible": False, "quality": 0.001} + assert "level" not in HTJ2K_PRESETS["balanced"] + assert _preset_encode_options( + {"preset": "balanced"}, + codec=CODEC_HTJ2K_OPENJPH, + ) == {"reversible": False, "quality": 0.0002} + assert _preset_encode_options( + {"preset": "balanced"}, + codec=CODEC_JPEG2K, + ) == {"reversible": False, "level": 100} + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_htj2k_balanced_preset_produces_reasonable_chunk_size() -> None: + plane = mandelbrot_plane(256) + options = _preset_encode_options( + {"preset": "balanced"}, + codec=CODEC_HTJ2K_OPENJPH, + ) + encoded = encode_image_plane(plane, CODEC_HTJ2K_OPENJPH, options) + assert 1_000 < len(encoded) < plane.nbytes + + +def test_recompress_spatialdata_rewrites_image_and_labels(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": {"morphology": {"preset": "lossless", "chunks": [1, 4, 4]}}, + "default_labels": {"codec": "blosc", "clevel": 5}, + }, + ) + + assert (result.store_path / "tables" / "table" / "zarr.json").exists() + image_meta = json.loads( + (result.store_path / "images" / "morphology" / "0" / "zarr.json").read_text() + ) + assert image_meta["codecs"] == [{"name": "imagecodecs_jpeg2k", "configuration": {}}] + assert image_meta["chunk_grid"]["configuration"]["chunk_shape"] == [1, 4, 4] + + first_chunk = result.manifest["images"][0]["chunks_checked"][0] + encoded = result.store_path / "images" / "morphology" / "0" / "c" / "0" / "0" / "0" + decoded = imagecodecs.jpeg2k_decode(encoded.read_bytes()) + assert first_chunk["source_sha256"] == first_chunk["decoded_sha256"] + assert int(decoded[0, 0]) == 0 + + label_meta = json.loads( + (result.store_path / "labels" / "cells" / "0" / "zarr.json").read_text() + ) + assert [codec["name"] for codec in label_meta["codecs"]] == ["bytes", "blosc"] + assert result.manifest_path is not None + assert result.manifest_path.exists() + + +def test_recompress_spatialdata_rejects_browser_unsupported_jp2k_dtype(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr", image_dtype="uint32") + + with pytest.raises(TypeError, match="<=16-bit integer"): + recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={"images": {"morphology": {"preset": "lossless"}}}, + ) + + +def test_recompress_preserves_root_spatialdata_attrs(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + original_attrs = json.loads((source / "zarr.json").read_text())["attributes"] + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": {"morphology": {"preset": "lossless", "chunks": [1, 4, 4]}}, + "default_labels": {"codec": None}, + }, + ) + + preserved = json.loads((result.store_path / "zarr.json").read_text())["attributes"] + assert preserved == original_attrs + + +def test_recompress_sibling_keeps_original_and_adds_new_group(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": {"morphology": {"preset": "lossless", "chunks": [1, 4, 4]}}, + "default_labels": {"codec": None}, + }, + sibling=True, + ) + + # Original group is untouched — still has its original zarr metadata (no JP2K codec). + original_meta = json.loads( + (result.store_path / "images" / "morphology" / "0" / "zarr.json").read_text() + ) + assert original_meta["codecs"] != [{"name": "imagecodecs_jpeg2k", "configuration": {}}] + + # Sibling group exists with the encoding-annotated name. + sibling_key = "morphology:jp2k_lossless" + sibling_meta = json.loads( + (result.store_path / "images" / sibling_key / "0" / "zarr.json").read_text() + ) + assert sibling_meta["codecs"] == [{"name": "imagecodecs_jpeg2k", "configuration": {}}] + + # Manifest records the sibling path, not the original. + assert result.manifest["images"][0]["path"] == f"images/{sibling_key}/0" + + +def test_lossy_preset_records_non_lossless_manifest(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": {"morphology": {"preset": "small", "chunks": [1, 4, 4]}}, + "default_labels": {"codec": None}, + }, + ) + + image_report = result.manifest["images"][0] + assert image_report["preset"] == "small" + assert image_report["lossless"] is False + assert image_report["encode_options"]["reversible"] is False + + +def test_recompress_rejects_unknown_image_codec(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + with pytest.raises(ValueError, match="Unsupported image codec"): + recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={"images": {"morphology": {"codec": "imagecodecs_jxl"}}}, + ) + + +@pytest.mark.skipif( + htj2k_encode_available(), + reason="HTJ2K encode is available; unavailable-path test not applicable.", +) +def test_recompress_rejects_htj2k_when_encode_unavailable(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + with pytest.raises(RuntimeError, match="HTJ2K recompression requested"): + recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": { + "morphology": { + "codec": CODEC_HTJ2K_OPENJPH, + "preset": "lossless", + "chunks": [1, 4, 4], + } + }, + "default_labels": {"codec": None}, + }, + ) + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_recompress_spatialdata_rewrites_image_with_htj2k(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": { + "morphology": { + "codec": CODEC_HTJ2K_OPENJPH, + "preset": "lossless", + "chunks": [1, 4, 4], + } + }, + "default_labels": {"codec": None}, + }, + ) + + image_meta = json.loads( + (result.store_path / "images" / "morphology" / "0" / "zarr.json").read_text() + ) + assert image_meta["codecs"] == [ + {"name": CODEC_HTJ2K_OPENJPH, "configuration": {}} + ] + + first_chunk = result.manifest["images"][0]["chunks_checked"][0] + encoded = result.store_path / "images" / "morphology" / "0" / "c" / "0" / "0" / "0" + decoded = decode_htj2k_plane(encoded.read_bytes()) + assert first_chunk["source_sha256"] == first_chunk["decoded_sha256"] + assert int(decoded[0, 0]) == 0 + assert result.manifest["images"][0]["codec"] == CODEC_HTJ2K_OPENJPH + assert result.manifest["images"][0]["encoder"] == "openjph-wasm" + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_recompress_sibling_uses_htj2k_key(tmp_path: Path) -> None: + source = _write_source_store(tmp_path / "source.zarr") + + result = recompress_spatialdata( + source, + tmp_path / "out.zarr", + config={ + "images": { + "morphology": { + "codec": CODEC_HTJ2K_OPENJPH, + "preset": "balanced", + "chunks": [1, 4, 4], + } + }, + "default_labels": {"codec": None}, + }, + sibling=True, + ) + + sibling_key = "morphology:htj2k_balanced" + sibling_meta = json.loads( + (result.store_path / "images" / sibling_key / "0" / "zarr.json").read_text() + ) + assert sibling_meta["codecs"] == [ + {"name": CODEC_HTJ2K_OPENJPH, "configuration": {}} + ] + assert result.manifest["images"][0]["path"] == f"images/{sibling_key}/0" diff --git a/python/spatialdata-codec-writer/tests/test_synthetic_images.py b/python/spatialdata-codec-writer/tests/test_synthetic_images.py new file mode 100644 index 00000000..fb73f8ef --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_synthetic_images.py @@ -0,0 +1,65 @@ +import numpy as np +import pytest + +from synthetic_images import fractal_tczyx_image, mandelbrot_plane, volume_tczyx + + +def _reference_mandelbrot_plane(size: int) -> np.ndarray: + plane = np.zeros((size, size), dtype=np.uint16) + for y in range(size): + for x in range(size): + cr = (x / size) * 3.5 - 2.5 + ci = (y / size) * 2.0 - 1.0 + zr = 0.0 + zi = 0.0 + iteration = 0 + while zr * zr + zi * zi <= 4.0 and iteration < 255: + nr = zr * zr - zi * zi + cr + zi = 2.0 * zr * zi + ci + zr = nr + iteration += 1 + plane[y, x] = (iteration * 16) % 4096 + return plane + + +def test_mandelbrot_plane_shape_and_dtype() -> None: + plane = mandelbrot_plane(32) + assert plane.shape == (32, 32) + assert plane.dtype == np.uint16 + + +def test_mandelbrot_plane_matches_reference_implementation() -> None: + size = 32 + assert np.array_equal(mandelbrot_plane(size), _reference_mandelbrot_plane(size)) + + +def test_fractal_tczyx_image_shape() -> None: + image = fractal_tczyx_image(64) + assert image.shape == (1, 1, 1, 64, 64) + + +def test_volume_tczyx_indexed_shape_and_slice_distinctness() -> None: + volume = volume_tczyx(8, t=2, c=1, z=3, pattern="indexed") + assert volume.shape == (2, 1, 3, 8, 8) + assert int(volume[0, 0, 0, 0, 0]) == 0 + assert int(volume[1, 0, 2, 0, 0]) == 1020 + assert int(volume[0, 0, 0, 0, 0]) != int(volume[1, 0, 2, 0, 0]) + + +def test_volume_tczyx_mandelbulb_smoke() -> None: + volume = volume_tczyx(16, t=2, c=1, z=3, pattern="mandelbulb") + assert volume.shape == (2, 1, 3, 16, 16) + assert volume.dtype == np.uint16 + assert np.all(volume <= 4095) + assert not np.array_equal(volume[0, 0, 0], volume[0, 0, 2]) + assert not np.array_equal(volume[0, 0, 0], volume[1, 0, 0]) + + +def test_volume_tczyx_rejects_non_positive_dimensions() -> None: + with pytest.raises(ValueError): + volume_tczyx(8, t=0, z=1) + + +def test_volume_tczyx_rejects_unsupported_pattern() -> None: + with pytest.raises(ValueError, match="Unsupported pattern 'typo'"): + volume_tczyx(8, pattern="typo") diff --git a/python/spatialdata-codec-writer/tests/test_write_synthetic.py b/python/spatialdata-codec-writer/tests/test_write_synthetic.py new file mode 100644 index 00000000..98ecb16b --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_write_synthetic.py @@ -0,0 +1,43 @@ +from __future__ import annotations + +import json +from pathlib import Path + +import pytest + +from spatialdata_codec_writer.htj2k_encode import htj2k_encode_available + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_write_synthetic_cli(tmp_path: Path) -> None: + from write_synthetic import main + + output = tmp_path / "indexed.zarr" + main( + [ + str(output), + "--pattern", + "indexed", + "--size", + "16", + "--t", + "2", + "--z", + "3", + "--image-key", + "synthetic", + "--chunks", + "1", + "1", + "1", + "16", + "16", + ] + ) + + manifest = json.loads(output.with_suffix(".manifest.json").read_text()) + assert manifest["shape"] == [2, 1, 3, 16, 16] + assert manifest["codec"] == "experimental.openjph_htj2k" diff --git a/python/spatialdata-codec-writer/tests/test_writer.py b/python/spatialdata-codec-writer/tests/test_writer.py new file mode 100644 index 00000000..ceca106d --- /dev/null +++ b/python/spatialdata-codec-writer/tests/test_writer.py @@ -0,0 +1,148 @@ +from pathlib import Path + +import imagecodecs +import json +import numpy as np +import pytest + +from spatialdata_codec_writer import htj2k_encode_available +from spatialdata_codec_writer.codecs import decode_htj2k_plane + +from fixture_writer import ( + image_to_tczyx, + write_codec_spatialdata, + write_codec_spatialdata_image, + write_jpeg2k_fixture, +) +from htj2k_fixtures import write_htj2k_fixture +from mandelbulb_fixtures import ( + MANDELBULB_FIXTURE_CHUNKS, + MANDELBULB_FIXTURE_IMAGE_KEY, + write_mandelbulb_fixture, +) +from provenance import experimental_codec_writer_attrs + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_write_htj2k_fixture(tmp_path: Path) -> None: + fixture = write_htj2k_fixture(tmp_path / "htj2k.zarr") + + assert fixture.store_path.exists() + assert fixture.manifest_path.exists() + assert fixture.manifest["codec"] == "experimental.openjph_htj2k" + assert fixture.manifest["encoder"] == "openjph-wasm" + + root_attrs = json.loads((fixture.store_path / "zarr.json").read_text())["attributes"] + assert root_attrs["spatialdata_attrs"] == experimental_codec_writer_attrs() + + first_chunk = fixture.manifest["chunks_checked"][0] + encoded = (fixture.store_path / first_chunk["path"]).read_bytes() + decoded = decode_htj2k_plane(encoded) + + assert decoded.shape == (32, 32) + assert int(decoded[0, 0]) == first_chunk["samples"][0] + + +class FakeImage: + def __init__(self, data: np.ndarray, dims: tuple[str, ...]) -> None: + self.data = data + self.dims = dims + + +class FakeSpatialData: + def __init__(self, image_key: str, image: FakeImage) -> None: + self.images = {image_key: image} + + +def test_write_jpeg2k_fixture(tmp_path: Path) -> None: + fixture = write_jpeg2k_fixture(tmp_path / "jpeg2k.zarr") + + assert fixture.store_path.exists() + assert fixture.manifest_path.exists() + assert fixture.manifest["codec"] == "imagecodecs_jpeg2k" + + first_chunk = fixture.manifest["chunks_checked"][0] + encoded = (fixture.store_path / first_chunk["path"]).read_bytes() + decoded = imagecodecs.jpeg2k_decode(encoded) + + assert decoded.shape == (32, 32) + assert int(decoded[0, 0]) == first_chunk["samples"][0] + + +@pytest.mark.skipif( + not htj2k_encode_available(), + reason="No HTJ2K encoder is available in this environment.", +) +def test_write_mandelbulb_fixture(tmp_path: Path) -> None: + fixture = write_mandelbulb_fixture(tmp_path / "mandelbulb.zarr") + + assert fixture.store_path.exists() + assert fixture.manifest_path.exists() + assert fixture.manifest["codec"] == "experimental.openjph_htj2k" + assert fixture.manifest["encoder"] == "openjph-wasm" + assert fixture.manifest["image_path"] == f"images/{MANDELBULB_FIXTURE_IMAGE_KEY}" + assert fixture.manifest["shape"] == [2, 1, 8, 128, 128] + assert list(fixture.manifest["chunks"]) == list(MANDELBULB_FIXTURE_CHUNKS) + + first_chunk = fixture.manifest["chunks_checked"][0] + encoded = (fixture.store_path / first_chunk["path"]).read_bytes() + decoded = decode_htj2k_plane(encoded) + + assert decoded.shape == (128, 128) + assert int(decoded[0, 0]) == first_chunk["samples"][0] + + +def test_image_to_tczyx_uses_named_dimensions() -> None: + image = FakeImage(np.arange(40, dtype=np.uint16).reshape(2, 4, 5), ("c", "y", "x")) + + normalized = image_to_tczyx(image) + + assert normalized.shape == (1, 2, 1, 4, 5) + assert int(normalized[0, 1, 0, 3, 4]) == 39 + + +def test_image_to_tczyx_uses_base_scale_for_multiscale_spatialdata_image() -> None: + from spatialdata.models import Image2DModel + + image = Image2DModel.parse( + np.arange(64, dtype=np.uint16).reshape(1, 8, 8), + dims=("c", "y", "x"), + scale_factors=[2], + ) + + normalized = image_to_tczyx(image) + + assert normalized.shape == (1, 1, 1, 8, 8) + assert int(normalized[0, 0, 0, 7, 7]) == 63 + + +def test_write_codec_spatialdata_accepts_named_image_key(tmp_path: Path) -> None: + image = FakeImage(np.arange(40, dtype=np.uint16).reshape(2, 4, 5), ("c", "y", "x")) + + fixture = write_codec_spatialdata( + tmp_path / "named.zarr", + image=image, + image_key="histology", + chunks=(1, 1, 1, 4, 5), + ) + + assert fixture.manifest["image_path"] == "images/histology" + assert (fixture.store_path / "images" / "histology" / "zarr.json").exists() + + +def test_write_codec_spatialdata_image_transcodes_existing_image(tmp_path: Path) -> None: + image = FakeImage(np.arange(40, dtype=np.uint16).reshape(2, 4, 5), ("c", "y", "x")) + sdata = FakeSpatialData("histology", image) + + fixture = write_codec_spatialdata_image( + tmp_path / "transcoded.zarr", + sdata, + image_key="histology", + chunks=(1, 1, 1, 4, 5), + ) + + assert fixture.manifest["image_path"] == "images/histology" + assert fixture.manifest["shape"] == [1, 2, 1, 4, 5] diff --git a/python/spatialdata-codec-writer/uv.lock b/python/spatialdata-codec-writer/uv.lock new file mode 100644 index 00000000..51b022d1 --- /dev/null +++ b/python/spatialdata-codec-writer/uv.lock @@ -0,0 +1,2526 @@ +version = 1 +revision = 3 +requires-python = ">=3.12" + +[[package]] +name = "aiobotocore" +version = "3.7.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "aiohttp" }, + { name = "aioitertools" }, + { name = "botocore" }, + { name = "jmespath" }, + { name = 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for Python spatialdata-codec-writer. + * + * stdin: JSON { width, height, dtype, reversible?, quality?, plane: base64 } + * stdout: raw HTJ2K bytes + * stderr: errors + */ +import { existsSync } from 'node:fs'; +import { fileURLToPath, pathToFileURL } from 'node:url'; +import { dirname, join } from 'node:path'; + +const repoRoot = join(dirname(fileURLToPath(import.meta.url)), '..'); + +function resolveOpenJphRoot() { + const candidates = [ + join(repoRoot, 'node_modules', '@cornerstonejs', 'codec-openjph'), + join(repoRoot, 'packages', 'zarrextra', 'node_modules', '@cornerstonejs', 'codec-openjph'), + ]; + for (const candidate of candidates) { + if (existsSync(join(candidate, 'dist', 'openjphjs.js'))) { + return candidate; + } + } + throw new Error( + 'Could not find @cornerstonejs/codec-openjph. Install monorepo dependencies with pnpm install.' + ); +} + +async function readStdin() { + const chunks = []; + for await (const chunk of process.stdin) { + chunks.push(chunk); + } + return Buffer.concat(chunks); +} + +function planeArrayForDtype(dtype, bytes) { + switch (dtype) { + case 'uint8': + return new Uint8Array(bytes.buffer, bytes.byteOffset, bytes.byteLength); + case 'int8': + return new Int8Array(bytes.buffer, bytes.byteOffset, bytes.byteLength); + case 'uint16': + return new Uint16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + case 'int16': + return new Int16Array(bytes.buffer, bytes.byteOffset, bytes.byteLength / 2); + default: + throw new Error(`Unsupported plane dtype '${dtype}'.`); + } +} + +async function loadEncoder() { + const openjphRoot = resolveOpenJphRoot(); + const mod = await import(pathToFileURL(join(openjphRoot, 'dist/openjphjs.js')).href); + const factory = mod.default ?? mod.OpenJPHJS ?? mod; + if (typeof factory !== 'function') { + throw new Error('Could not load OpenJPH WASM factory.'); + } + const wasmPath = join(openjphRoot, 'dist/openjphjs.wasm'); + return await factory({ + locateFile: (path) => (path.endsWith('.wasm') ? wasmPath : path), + }); +} + +async function encodePlane(runtime, request) { + const Encoder = runtime.HTJ2KEncoder; + if (!Encoder) { + throw new Error('OpenJPH runtime does not expose HTJ2KEncoder.'); + } + + const { width, height, dtype } = request; + const reversible = request.reversible ?? true; + const quality = request.quality ?? 0; + const planeBytes = Buffer.from(request.plane, 'base64'); + const plane = planeArrayForDtype(dtype, planeBytes); + const expectedValues = width * height; + if (plane.length !== expectedValues) { + throw new Error(`Plane has ${plane.length} samples, expected ${expectedValues}.`); + } + + const frame = { + width, + height, + bitsPerSample: dtype === 'uint8' || dtype === 'int8' ? 8 : 16, + isSigned: dtype === 'int8' || dtype === 'int16', + componentCount: 1, + isUsingColorTransform: false, + }; + + const encoder = new Encoder(); + encoder.setQuality(reversible, quality); + const buffer = encoder.getDecodedBuffer(frame); + const target = + frame.bitsPerSample === 16 + ? new Uint16Array(buffer.buffer, buffer.byteOffset, plane.length) + : new Uint8Array(buffer.buffer, buffer.byteOffset, plane.length); + target.set(plane); + encoder.encode(); + return encoder.getEncodedBuffer(); +} + +async function main() { + const runtime = await loadEncoder(); + const request = JSON.parse((await readStdin()).toString('utf8')); + const encoded = await encodePlane(runtime, request); + process.stdout.write(Buffer.from(encoded)); +} + +main().catch((error) => { + const message = error instanceof Error ? error.message : String(error); + process.stderr.write(`${message}\n`); + process.exit(1); +}); diff --git a/scripts/vendor-openjph-for-python.mjs b/scripts/vendor-openjph-for-python.mjs new file mode 100644 index 00000000..f7562760 --- /dev/null +++ b/scripts/vendor-openjph-for-python.mjs @@ -0,0 +1,52 @@ +#!/usr/bin/env node +/** + * Copy @cornerstonejs/codec-openjph dist assets into spatialdata-codec-writer + * package data for standalone pip installs (no monorepo checkout required). + */ +import { copyFileSync, existsSync, mkdirSync } from 'node:fs'; +import { dirname, join } from 'node:path'; +import { fileURLToPath } from 'node:url'; + +const repoRoot = join(dirname(fileURLToPath(import.meta.url)), '..'); + +function resolveOpenJphRoot() { + const candidates = [ + join(repoRoot, 'node_modules', '@cornerstonejs', 'codec-openjph'), + join(repoRoot, 'packages', 'zarrextra', 'node_modules', '@cornerstonejs', 'codec-openjph'), + ]; + for (const candidate of candidates) { + if (existsSync(join(candidate, 'dist', 'openjphjs.js'))) { + return candidate; + } + } + throw new Error( + 'Could not find @cornerstonejs/codec-openjph. Run pnpm install at the repository root.' + ); +} + +const openjphRoot = resolveOpenJphRoot(); +const vendorRoot = join( + repoRoot, + 'python', + 'spatialdata-codec-writer', + 'src', + 'spatialdata_codec_writer', + 'vendor', + 'openjph' +); +mkdirSync(vendorRoot, { recursive: true }); + +const requiredArtifacts = ['openjphjs.js', 'openjphjs.wasm']; +for (const name of requiredArtifacts) { + const source = join(openjphRoot, 'dist', name); + if (!existsSync(source)) { + throw new Error(`Required OpenJPH artifact not found: ${source}`); + } +} + +for (const name of requiredArtifacts) { + const source = join(openjphRoot, 'dist', name); + const dest = join(vendorRoot, name); + copyFileSync(source, dest); + console.log(`Vendored ${name} -> ${dest}`); +} diff --git a/tests/integration/codecFixtures.test.ts b/tests/integration/codecFixtures.test.ts new file mode 100644 index 00000000..5b55bb06 --- /dev/null +++ b/tests/integration/codecFixtures.test.ts @@ -0,0 +1,169 @@ +import { execSync } from 'node:child_process'; +import { existsSync, mkdirSync, readFileSync } from 'node:fs'; +import { dirname, join } from 'node:path'; +import { fileURLToPath } from 'node:url'; +import { FileSystemStore } from '@zarrita/storage'; +import { describe, expect, it } from 'vitest'; +import { readZarr } from '../../packages/core/src/store/index.js'; +import { + loadOmeZarrMultiscalesFromStore, + registerExperimentalHtj2kCodec, + registerJpeg2kCodec, +} from '../../packages/zarrextra/src/index.js'; + +const __filename = fileURLToPath(import.meta.url); +const __dirname = dirname(__filename); +const projectRoot = join(__dirname, '../..'); +const uvCacheDir = join(projectRoot, '.tmp', 'uv-cache'); +const fixtureDir = join(projectRoot, 'test-fixtures', 'codecs'); +const jpeg2kFixturePath = join(fixtureDir, 'jpeg2k.zarr'); +const jpeg2kManifestPath = join(fixtureDir, 'jpeg2k.manifest.json'); +const mandelbulbFixturePath = join(fixtureDir, 'mandelbulb.zarr'); +const mandelbulbManifestPath = join(fixtureDir, 'mandelbulb.manifest.json'); +const htj2kFixturePath = join(fixtureDir, 'htj2k.zarr'); +const htj2kManifestPath = join(fixtureDir, 'htj2k.manifest.json'); + +function ensureCodecFixture() { + const hasJpeg2k = existsSync(jpeg2kFixturePath) && existsSync(jpeg2kManifestPath); + const hasMandelbulb = existsSync(mandelbulbFixturePath) && existsSync(mandelbulbManifestPath); + if (hasJpeg2k && hasMandelbulb) { + return; + } + mkdirSync(uvCacheDir, { recursive: true }); + execSync( + `node scripts/vendor-openjph-for-python.mjs && uv run --directory python/spatialdata-codec-writer python scripts/generate_codec_fixtures.py --output-dir ${JSON.stringify(fixtureDir)} --experimental-htj2k --overwrite`, + { + cwd: projectRoot, + env: { + ...process.env, + UV_CACHE_DIR: uvCacheDir, + }, + stdio: 'inherit', + } + ); +} + +describe('codec fixtures', () => { + it('generates a Python reference fixture that readZarr can parse', async () => { + ensureCodecFixture(); + + const sdata = await readZarr(new FileSystemStore(jpeg2kFixturePath)); + expect(sdata.images).toBeDefined(); + expect(sdata.images?.codec_image).toBeDefined(); + expect(sdata.images?.codec_image.scaleLevels).toEqual(['0', '1']); + + const manifest = JSON.parse(readFileSync(jpeg2kManifestPath, 'utf8')); + expect(manifest.codec).toBe('imagecodecs_jpeg2k'); + expect(manifest.shape).toEqual([1, 1, 1, 64, 64]); + }, 180000); + + it('reports unknown codec before JPEG2K registration', async () => { + ensureCodecFixture(); + + const sdata = await readZarr(new FileSystemStore(jpeg2kFixturePath)); + const store = sdata.images?.codec_image.getStore(); + expect(store).toBeDefined(); + if (!store) throw new Error('Expected codec_image store to be available.'); + const [source] = await loadOmeZarrMultiscalesFromStore(store); + await expect(source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } })).rejects.toThrow( + /Unknown codec/ + ); + }, 180000); + + it('can decode the JP2K fixture when the optional WASM decoder is installed', async () => { + ensureCodecFixture(); + try { + await import('@cornerstonejs/codec-openjpeg/decode'); + } catch { + console.warn( + 'Skipping JP2K decode smoke test: @cornerstonejs/codec-openjpeg is not installed.' + ); + return; + } + + registerJpeg2kCodec(); + const sdata = await readZarr(new FileSystemStore(jpeg2kFixturePath)); + const image = sdata.images?.codec_image; + expect(image).toBeDefined(); + if (!image) throw new Error('Expected codec_image to be available.'); + const [source] = await loadOmeZarrMultiscalesFromStore(image.getStore()); + const tile = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + const manifest = JSON.parse(readFileSync(jpeg2kManifestPath, 'utf8')); + + expect(tile.width).toBe(32); + expect(tile.height).toBe(32); + expect(Number((tile.data as Uint16Array)[0])).toBe(manifest.chunks_checked[0].samples[0]); + }, 180000); + + it('can decode the Mandelbulb HTJ2K fixture across t/z selections', async () => { + ensureCodecFixture(); + if (!existsSync(mandelbulbFixturePath) || !existsSync(mandelbulbManifestPath)) { + console.warn( + 'Skipping Mandelbulb HTJ2K decode smoke test: mandelbulb.zarr was not generated (OpenJPH WASM encoder unavailable).' + ); + return; + } + try { + await import('@cornerstonejs/codec-openjph'); + } catch { + console.warn( + 'Skipping Mandelbulb HTJ2K decode smoke test: @cornerstonejs/codec-openjph is not installed.' + ); + return; + } + + registerExperimentalHtj2kCodec(); + const sdata = await readZarr(new FileSystemStore(mandelbulbFixturePath)); + const image = sdata.images?.mandelbulb; + expect(image).toBeDefined(); + if (!image) throw new Error('Expected mandelbulb image to be available.'); + + const manifest = JSON.parse(readFileSync(mandelbulbManifestPath, 'utf8')); + expect(manifest.codec).toBe('experimental.openjph_htj2k'); + expect(manifest.shape).toEqual([2, 1, 8, 128, 128]); + + const [source] = await loadOmeZarrMultiscalesFromStore(image.getStore()); + expect(source.shape).toEqual([2, 1, 8, 128, 128]); + + const tileTz0 = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + const tileTz1 = await source.getTile({ x: 0, y: 0, selection: { t: 1, c: 0, z: 2 } }); + + expect(tileTz0.width).toBe(128); + expect(tileTz0.height).toBe(128); + expect(Number((tileTz0.data as Uint16Array)[0])).toBe(manifest.chunks_checked[0].samples[0]); + expect(Number((tileTz1.data as Uint16Array)[0])).not.toBe( + Number((tileTz0.data as Uint16Array)[0]) + ); + }, 180000); + + it('can decode the HTJ2K fixture when the optional WASM decoder is installed', async () => { + ensureCodecFixture(); + if (!existsSync(htj2kFixturePath) || !existsSync(htj2kManifestPath)) { + console.warn( + 'Skipping HTJ2K decode smoke test: htj2k.zarr was not generated (OpenJPH WASM encoder unavailable).' + ); + return; + } + try { + await import('@cornerstonejs/codec-openjph'); + } catch { + console.warn( + 'Skipping HTJ2K decode smoke test: @cornerstonejs/codec-openjph is not installed.' + ); + return; + } + + registerExperimentalHtj2kCodec(); + const sdata = await readZarr(new FileSystemStore(htj2kFixturePath)); + const image = sdata.images?.codec_image; + expect(image).toBeDefined(); + if (!image) throw new Error('Expected codec_image to be available.'); + const [source] = await loadOmeZarrMultiscalesFromStore(image.getStore()); + const tile = await source.getTile({ x: 0, y: 0, selection: { t: 0, c: 0, z: 0 } }); + const manifest = JSON.parse(readFileSync(htj2kManifestPath, 'utf8')); + + expect(tile.width).toBe(32); + expect(tile.height).toBe(32); + expect(Number((tile.data as Uint16Array)[0])).toBe(manifest.chunks_checked[0].samples[0]); + }, 180000); +}); diff --git a/vite.config.base.ts b/vite.config.base.ts index cf72a600..1aa2cacf 100644 --- a/vite.config.base.ts +++ b/vite.config.base.ts @@ -1,17 +1,44 @@ +import path from 'node:path'; import { defineConfig } from 'vite'; import react from '@vitejs/plugin-react'; import dts from 'vite-plugin-dts'; -import path from 'node:path'; -export function createWorkspaceSourceAliases(rootDir: string) { - return { - '@spatialdata/avivatorish': path.resolve(rootDir, 'packages/avivatorish/src/index.ts'), - '@spatialdata/core': path.resolve(rootDir, 'packages/core/src/index.ts'), - '@spatialdata/layers': path.resolve(rootDir, 'packages/layers/src/index.ts'), - '@spatialdata/react': path.resolve(rootDir, 'packages/react/src/index.ts'), - '@spatialdata/vis': path.resolve(rootDir, 'packages/vis/src/index.ts'), - zarrextra: path.resolve(rootDir, 'packages/zarrextra/src/index.ts'), - }; +export type WorkspaceAlias = { + find: string | RegExp; + replacement: string; +}; + +export function createWorkspaceSourceAliases(rootDir: string): WorkspaceAlias[] { + return [ + { + find: 'zarrextra/workers', + replacement: path.resolve(rootDir, 'packages/zarrextra/src/workers/index.ts'), + }, + { + find: /^zarrextra$/, + replacement: path.resolve(rootDir, 'packages/zarrextra/src/index.ts'), + }, + { + find: '@spatialdata/avivatorish', + replacement: path.resolve(rootDir, 'packages/avivatorish/src/index.ts'), + }, + { + find: '@spatialdata/core', + replacement: path.resolve(rootDir, 'packages/core/src/index.ts'), + }, + { + find: '@spatialdata/layers', + replacement: path.resolve(rootDir, 'packages/layers/src/index.ts'), + }, + { + find: '@spatialdata/react', + replacement: path.resolve(rootDir, 'packages/react/src/index.ts'), + }, + { + find: '@spatialdata/vis', + replacement: path.resolve(rootDir, 'packages/vis/src/index.ts'), + }, + ]; } interface DefineConfigOptions { @@ -28,20 +55,13 @@ export function defineViteConfig(options: DefineConfigOptions) { plugins: [ react(), dts({ - // Keep the plugin fully anchored to this package root: pkgRoot, tsconfigPath: path.resolve(pkgRoot, 'tsconfig.json'), - - // Emit types into dist and make a top-level index.d.ts outDir: path.resolve(pkgRoot, 'dist'), - entryRoot: 'src', // IMPORTANT: relative to root, not absolute + entryRoot: 'src', insertTypesEntry: true, strictOutput: true, - - // Don’t rewrite tsconfig "paths" to relative imports pathsToAliases: false, - - // Only process source; keep configs/tests out include: ['src'], exclude: [ 'dist/**', @@ -51,9 +71,6 @@ export function defineViteConfig(options: DefineConfigOptions) { '**/*.spec.*', '**/*.stories.*', ], - - // Optional: if you don’t want .d.ts.map files - // compilerOptions: { declarationMap: false }, }), ], build: {