refactor: move the density clustering code to its own internal package

.gitignore

@@ -6,7 +6,6 @@ build/
 dist/
 distlib/
 target/
-pkg/
 .svelte-kit/
 .env
 .env.*

package.json

@@ -5,6 +5,7 @@
     "packages/viewer",
     "packages/table",
     "packages/umap-wasm",
+    "packages/density-clustering",
     "packages/embedding-atlas",
     "packages/examples",
     "packages/backend",

packages/component/src/lib/embedding_view/worker/worker_functions.ts

@@ -1,6 +1,6 @@
 // Copyright (c) 2025 Apple Inc. Licensed under MIT License.
 
-import { findClusters } from "../../density_clustering/find_clusters.js";
+import { findClusters } from "@embedding-atlas/density-clustering";
 import { dynamicLabelPlacement } from "../../dynamic_label_placement/dynamic_label_placement.js";
 
 export { dynamicLabelPlacement, findClusters };

packages/component/src/lib/index.ts

@@ -8,8 +8,6 @@ export {
   type EmbeddingViewProps,
 } from "./embedding_view/api.js";
 
-export { findClusters, type Cluster, type FindClustersOptions } from "./density_clustering/find_clusters.js";
-
 export { defaultCategoryColors } from "./colors.js";
 
 export type { Theme } from "./embedding_view/theme.js";

packages/density-clustering/density_clustering_wasm/js/index.d.ts

@@ -0,0 +1,42 @@
+/** A resulting cluster from the find clusters function */
+export interface Cluster {
+  /** Cluster identifier */
+  identifier: number;
+  /** The total density */
+  sum_density: number;
+  /** The mean x location (weighted by density) */
+  mean_x: number;
+  /** The mean y location (weighted by density) */
+  mean_y: number;
+  /** The maximum density */
+  max_density: number;
+  /** The location with the maximum density */
+  max_density_location: [number, number];
+  /** The number of pixels in the cluster */
+  pixel_count: number;
+  /** The cluster's boundary represented as a list of polygons */
+  boundary?: [number, number][][];
+  /** The cluster's boundary approximated with a list of rectangles */
+  boundary_rect_approximation?: [number, number, number, number][];
+}
+
+/** Options of the find clusters function */
+export interface FindClustersOptions {
+  /** The threshold for unioning two clusters */
+  union_threshold: number;
+}
+
+/**
+ * Find clusters from a density map
+ * @param density_map the density map, a `Float32Array` with `width * height` elements
+ * @param width the width of the density map
+ * @param height the height of the density map
+ * @param options algorithm options
+ * @returns
+ */
+export async function findClusters(
+  density_map: Float32Array,
+  width: number,
+  height: number,
+  options: Partial<FindClustersOptions> = {},
+): Promise<Cluster[]>;

packages/component/src/lib/density_clustering/find_clusters.ts → packages/density-clustering/density_clustering_wasm/js/index.js

@@ -1,34 +1,6 @@
 // Copyright (c) 2025 Apple Inc. Licensed under MIT License.
 
-import * as cluster from "./wasm/density_clustering_wasm.js";
-
-/** A resulting cluster from the find clusters function */
-export interface Cluster {
-  /** Cluster identifier */
-  identifier: number;
-  /** The total density */
-  sum_density: number;
-  /** The mean x location (weighted by density) */
-  mean_x: number;
-  /** The mean y location (weighted by density) */
-  mean_y: number;
-  /** The maximum density */
-  max_density: number;
-  /** The location with the maximum density */
-  max_density_location: [number, number];
-  /** The number of pixels in the cluster */
-  pixel_count: number;
-  /** The cluster's boundary represented as a list of polygons */
-  boundary?: [number, number][][];
-  /** The cluster's boundary approximated with a list of rectangles */
-  boundary_rect_approximation?: [number, number, number, number][];
-}
-
-/** Options of the find clusters function */
-export interface FindClustersOptions {
-  /** The threshold for unioning two clusters */
-  union_threshold: number;
-}
+import * as cluster from "../pkg/density_clustering_wasm.js";
 
 /**
  * Find clusters from a density map
@@ -38,12 +10,7 @@ export interface FindClustersOptions {
  * @param options algorithm options
  * @returns
  */
-export async function findClusters(
-  density_map: Float32Array,
-  width: number,
-  height: number,
-  options: Partial<FindClustersOptions> = {},
-): Promise<Cluster[]> {
+export async function findClusters(density_map, width, height, options = {}) {
   await cluster.default();
   // console.debug(`find clusters start, size: ${width}x${height}`);
   let t0 = new Date().getTime();
@@ -62,7 +29,7 @@ export async function findClusters(
     smooth_boundaries: true,
   });
   input.free();
-  let clusters: Cluster[] = [];
+  let clusters = [];
   for (let [id, summary] of result.summaries) {
     clusters.push({
       identifier: id,

packages/component/src/lib/density_clustering/wasm/density_clustering_wasm.js → packages/density-clustering/density_clustering_wasm/pkg/density_clustering_wasm.js

@@ -1,40 +1,13 @@
 let wasm;
 
-const cachedTextDecoder = (typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8', { ignoreBOM: true, fatal: true }) : { decode: () => { throw Error('TextDecoder not available') } } );
-
-if (typeof TextDecoder !== 'undefined') { cachedTextDecoder.decode(); };
-
-let cachedUint8Memory0 = null;
-
-function getUint8Memory0() {
-    if (cachedUint8Memory0 === null || cachedUint8Memory0.byteLength === 0) {
-        cachedUint8Memory0 = new Uint8Array(wasm.memory.buffer);
-    }
-    return cachedUint8Memory0;
-}
-
-function getStringFromWasm0(ptr, len) {
-    ptr = ptr >>> 0;
-    return cachedTextDecoder.decode(getUint8Memory0().subarray(ptr, ptr + len));
-}
-
 const heap = new Array(128).fill(undefined);
 
 heap.push(undefined, null, true, false);
 
-let heap_next = heap.length;
-
-function addHeapObject(obj) {
-    if (heap_next === heap.length) heap.push(heap.length + 1);
-    const idx = heap_next;
-    heap_next = heap[idx];
-
-    heap[idx] = obj;
-    return idx;
-}
-
 function getObject(idx) { return heap[idx]; }
 
+let heap_next = heap.length;
+
 function dropObject(idx) {
     if (idx < 132) return;
     heap[idx] = heap_next;
@@ -69,6 +42,33 @@ function getInt32Memory0() {
     return cachedInt32Memory0;
 }
 
+const cachedTextDecoder = (typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8', { ignoreBOM: true, fatal: true }) : { decode: () => { throw Error('TextDecoder not available') } } );
+
+if (typeof TextDecoder !== 'undefined') { cachedTextDecoder.decode(); };
+
+let cachedUint8Memory0 = null;
+
+function getUint8Memory0() {
+    if (cachedUint8Memory0 === null || cachedUint8Memory0.byteLength === 0) {
+        cachedUint8Memory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8Memory0;
+}
+
+function getStringFromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return cachedTextDecoder.decode(getUint8Memory0().subarray(ptr, ptr + len));
+}
+
+function addHeapObject(obj) {
+    if (heap_next === heap.length) heap.push(heap.length + 1);
+    const idx = heap_next;
+    heap_next = heap[idx];
+
+    heap[idx] = obj;
+    return idx;
+}
+
 let WASM_VECTOR_LEN = 0;
 
 const cachedTextEncoder = (typeof TextEncoder !== 'undefined' ? new TextEncoder('utf-8') : { encode: () => { throw Error('TextEncoder not available') } } );
@@ -303,10 +303,6 @@ async function __wbg_load(module, imports) {
 function __wbg_get_imports() {
     const imports = {};
     imports.wbg = {};
-    imports.wbg.__wbindgen_error_new = function(arg0, arg1) {
-        const ret = new Error(getStringFromWasm0(arg0, arg1));
-        return addHeapObject(ret);
-    };
     imports.wbg.__wbindgen_boolean_get = function(arg0) {
         const v = getObject(arg0);
         const ret = typeof(v) === 'boolean' ? (v ? 1 : 0) : 2;
@@ -338,6 +334,10 @@ function __wbg_get_imports() {
         const ret = typeof(getObject(arg0)) === 'string';
         return ret;
     };
+    imports.wbg.__wbindgen_error_new = function(arg0, arg1) {
+        const ret = new Error(getStringFromWasm0(arg0, arg1));
+        return addHeapObject(ret);
+    };
     imports.wbg.__wbindgen_jsval_loose_eq = function(arg0, arg1) {
         const ret = getObject(arg0) == getObject(arg1);
         return ret;

packages/component/src/lib/density_clustering/wasm/density_clustering_wasm_bg.js → packages/density-clustering/density_clustering_wasm/pkg/density_clustering_wasm_bg.js

@@ -4,43 +4,14 @@ export function __wbg_set_wasm(val) {
 }
 
 
-const lTextDecoder = typeof TextDecoder === 'undefined' ? (0, module.require)('util').TextDecoder : TextDecoder;
-
-let cachedTextDecoder = new lTextDecoder('utf-8', { ignoreBOM: true, fatal: true });
-
-cachedTextDecoder.decode();
-
-let cachedUint8Memory0 = null;
-
-function getUint8Memory0() {
-    if (cachedUint8Memory0 === null || cachedUint8Memory0.byteLength === 0) {
-        cachedUint8Memory0 = new Uint8Array(wasm.memory.buffer);
-    }
-    return cachedUint8Memory0;
-}
-
-function getStringFromWasm0(ptr, len) {
-    ptr = ptr >>> 0;
-    return cachedTextDecoder.decode(getUint8Memory0().subarray(ptr, ptr + len));
-}
-
 const heap = new Array(128).fill(undefined);
 
 heap.push(undefined, null, true, false);
 
-let heap_next = heap.length;
-
-function addHeapObject(obj) {
-    if (heap_next === heap.length) heap.push(heap.length + 1);
-    const idx = heap_next;
-    heap_next = heap[idx];
-
-    heap[idx] = obj;
-    return idx;
-}
-
 function getObject(idx) { return heap[idx]; }
 
+let heap_next = heap.length;
+
 function dropObject(idx) {
     if (idx < 132) return;
     heap[idx] = heap_next;
@@ -75,6 +46,35 @@ function getInt32Memory0() {
     return cachedInt32Memory0;
 }
 
+const lTextDecoder = typeof TextDecoder === 'undefined' ? (0, module.require)('util').TextDecoder : TextDecoder;
+
+let cachedTextDecoder = new lTextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+
+cachedTextDecoder.decode();
+
+let cachedUint8Memory0 = null;
+
+function getUint8Memory0() {
+    if (cachedUint8Memory0 === null || cachedUint8Memory0.byteLength === 0) {
+        cachedUint8Memory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8Memory0;
+}
+
+function getStringFromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return cachedTextDecoder.decode(getUint8Memory0().subarray(ptr, ptr + len));
+}
+
+function addHeapObject(obj) {
+    if (heap_next === heap.length) heap.push(heap.length + 1);
+    const idx = heap_next;
+    heap_next = heap[idx];
+
+    heap[idx] = obj;
+    return idx;
+}
+
 let WASM_VECTOR_LEN = 0;
 
 const lTextEncoder = typeof TextEncoder === 'undefined' ? (0, module.require)('util').TextEncoder : TextEncoder;
@@ -277,11 +277,6 @@ export class DensityMap {
     }
 }
 
-export function __wbindgen_error_new(arg0, arg1) {
-    const ret = new Error(getStringFromWasm0(arg0, arg1));
-    return addHeapObject(ret);
-};
-
 export function __wbindgen_boolean_get(arg0) {
     const v = getObject(arg0);
     const ret = typeof(v) === 'boolean' ? (v ? 1 : 0) : 2;
@@ -320,6 +315,11 @@ export function __wbindgen_is_string(arg0) {
     return ret;
 };
 
+export function __wbindgen_error_new(arg0, arg1) {
+    const ret = new Error(getStringFromWasm0(arg0, arg1));
+    return addHeapObject(ret);
+};
+
 export function __wbindgen_jsval_loose_eq(arg0, arg1) {
     const ret = getObject(arg0) == getObject(arg1);
     return ret;

packages/density-clustering/package.json

@@ -0,0 +1,17 @@
+{
+  "name": "@embedding-atlas/density-clustering",
+  "version": "0.0.0",
+  "private": true,
+  "description": "A WebAssembly implementation of a density-based clustering algorithm",
+  "main": "density_clustering_wasm/js/index.js",
+  "module": "density_clustering_wasm/js/index.js",
+  "type": "module",
+  "scripts": {
+    "build": "npx wasm-pack build --release --target web density_clustering_wasm && rm density_clustering_wasm/pkg/.gitignore density_clustering_wasm/pkg/package.json"
+  },
+  "files": [
+    "density_clustering_wasm/js/index.js",
+    "density_clustering_wasm/pkg/density_clustering_wasm.js",
+    "density_clustering_wasm/pkg/density_clustering_wasm_bg.wasm"
+  ]
+}