Add zarr.js

.gitignore

@@ -1,2 +1,3 @@
 target*
 __pycache__/
+node_modules/

Makefile

@@ -20,7 +20,11 @@ z5py: data/reference_image.png
 zarr: data/reference_image.png
 	python generate_data/generate_zarr.py
 
+.PHONY: js
+js: data/reference_image.png
+	bash generate_data/js/generate_data.sh
+
 .PHONY: data
-data: n5java pyn5 z5py zarr
+data: n5java pyn5 z5py zarr js
 
 .PHONY: test

environment.yml

@@ -5,6 +5,7 @@ dependencies:
   - openjdk
   - maven
   - make
+  - nodejs
   - z5py >= 2.0.8
   - python == 3.7.9
   - scikit-image

generate_data/js/generate_data.sh

@@ -0,0 +1,6 @@
+# cd to this directory
+# https://stackoverflow.com/a/6393573/2700168
+cd "${0%/*}"
+
+npm install
+npm start

generate_data/js/package.json

@@ -0,0 +1,10 @@
+{
+  "type": "module",
+  "scripts": {
+    "start": "node src/index.js"
+  },
+  "dependencies": {
+    "pngjs": "^6.0.0",
+    "zarr": "^0.4.0"
+  }
+}

generate_data/js/src/fsstore.js

@@ -0,0 +1,37 @@
+import path from "path";
+import { promises as fsp } from "fs";
+import fs from "fs";
+
+import { KeyError } from "zarr";
+
+class FSStore {
+  constructor(root) {
+    this.root = root;
+    if (!fs.existsSync(root)) {
+      fs.mkdirSync(root, { recursive: true });
+    }
+  }
+
+  getItem(key) {
+    const fp = path.join(this.root, key);
+    return fsp.readFile(fp, null).catch((err) => {
+      if (err.code === "ENOENT") {
+        throw new KeyError(key);
+      }
+      throw err;
+    });
+  }
+
+  async setItem(key, value) {
+    const fp = path.join(this.root, key);
+    await fsp.mkdir(path.dirname(fp), { recursive: true });
+    await fsp.writeFile(fp, Buffer.from(value), null);
+  }
+
+  containsItem(key) {
+    const fp = path.join(this.root, key);
+    return fs.existsSync(fp);
+  }
+}
+
+export default FSStore;

generate_data/js/src/index.js

@@ -0,0 +1,53 @@
+import fs from "fs";
+import p from "path";
+import { PNG } from "pngjs";
+
+import { openGroup, NestedArray, slice } from "zarr";
+import FSStore from "./fsstore.js";
+
+const CHUNKS = [100, 100, 1];
+const STR_TO_COMPRESSOR = {
+  gzip: { id: "gzip", level: 1 },
+  blosc: { id: "blosc", cname: "lz4", clevel: 5, blocksize: 0, shuffle: 1 },
+  zlib: { id: "zlib", level: 1 },
+};
+
+// Simple convenience method to init the root for an empty store.
+async function open(path) {
+  const store = new FSStore(path);
+  const text = JSON.stringify({ zarr_format: 2 });
+  await store.setItem(".zgroup", Buffer.from(text));
+  return openGroup(store);
+}
+
+function imread(path) {
+  const buf = fs.readFileSync(path);
+  const { data, height, width } = PNG.sync.read(buf, { colorType: 2 });
+  const arr = new NestedArray(new Uint8Array(data), [height, width, 4]);
+  return arr.get([null, null, slice(3)]); // drop alpha channel
+}
+
+function getName(config) {
+  if (config === null) return "raw";
+  if (config.cname) return `${config.id}/${config.cname}`;
+  return config.id;
+}
+
+async function generateZarrFormat(codecIds = ["gzip", "blosc", "zlib", null]) {
+  const path = p.join("..", "..", "data", "js.zr");
+  const img = imread(p.join("..", "..", "data", "reference_image.png"));
+
+  fs.rmSync(path, { recursive: true, force: true });
+  const grp = await open(path);
+  for (const id of codecIds) {
+    const config = id ? STR_TO_COMPRESSOR[id] : null;
+    const name = getName(config);
+    grp.createDataset(name, undefined, img, {
+      compressor: config,
+      chunks: CHUNKS,
+      fillValue: 0,
+    });
+  }
+}
+
+generateZarrFormat();