[Feat] Typescript TRK reader for visualising Tractography Data

package.json

@@ -41,8 +41,10 @@
   },
   "devDependencies": {
     "@types/codemirror": "5.60.15",
+    "@types/dotenv": "^6.1.1",
     "@types/gl-matrix": "^2.4.5",
     "@types/lodash-es": "^4.17.12",
+    "@types/mathjs": "^9.4.1",
     "@types/node": "^20.14.12",
     "@types/pako": "^2.0.3",
     "@types/yargs": "^17.0.32",
@@ -53,7 +55,6 @@
     "css-loader": "^7.1.2",
     "esbuild": "^0.23.0",
     "esbuild-loader": "^4.2.2",
-    "eslint": "^8.56.0",
     "eslint-formatter-codeframe": "^7.32.1",
     "eslint-import-resolver-typescript": "^3.6.1",
     "eslint-interactive": "^10.8.0",
@@ -77,14 +78,20 @@
     "webpack-merge": "^6.0.1"
   },
   "dependencies": {
+    "axios": "^1.7.7",
+    "browserify-fs": "^1.0.0",
+    "buffer": "^6.0.3",
     "codemirror": "^5.61.1",
+    "dotenv": "^16.4.5",
     "gl-matrix": "3.1.0",
     "glsl-editor": "^1.0.0",
     "ikonate": "github:mikolajdobrucki/ikonate#a86b4107c6ec717e7877f880a930d1ccf0b59d89",
     "lodash-es": "^4.17.21",
+    "mathjs": "^13.2.0",
     "nifti-reader-js": "^0.6.8",
     "numcodecs": "^0.3.1",
-    "pako": "^2.1.0"
+    "pako": "^2.1.0",
+    "path-browserify": "^1.0.1"
   },
   "overrides": {
     "@puppeteer/browsers": ">=2"
@@ -96,8 +103,8 @@
   "type": "module",
   "exports": {
     ".": "./src/main_module.ts",
-    "./unstable/*.js": "./src/*.ts",
-    "./unstable/*": "./src/*"
+    "./*.js": "./src/*.ts",
+    "./*": "./src/*"
   },
   "imports": {
     "#src/third_party/jpgjs/jpg.js": "./src/third_party/jpgjs/jpg.js",
@@ -335,6 +342,24 @@
       "neuroglancer/datasource/render:disabled": "./src/datasource/render/register_default.ts",
       "default": "./src/datasource/render/register_default.ts"
     },
+    "#datasource/trk/backend": {
+      "neuroglancer/datasource/trk:enabled": "./src/datasource/trk/backend.ts",
+      "neuroglancer/datasource:none_by_default": "./src/util/false.ts",
+      "neuroglancer/datasource/trk:disabled": "./src/datasource/trk/backend.ts",
+      "default": "./src/datasource/trk/backend.ts"
+    },
+    "#datasource/trk/async_computation": {
+      "neuroglancer/datasource/trk:enabled": "./src/datasource/trk/async_computation.ts",
+      "neuroglancer/datasource:none_by_default": "./src/util/false.ts",
+      "neuroglancer/datasource/trk:disabled": "./src/datasource/trk/async_computation.ts",
+      "default": "./src/datasource/trk/async_computation.ts"
+    },
+    "#datasource/trk/register_default": {
+      "neuroglancer/datasource/trk:enabled": "./src/datasource/trk/register_default.ts",
+      "neuroglancer/datasource:none_by_default": "./src/util/false.ts",
+      "neuroglancer/datasource/trk:disabled": "./src/datasource/trk/register_default.ts",
+      "default": "./src/datasource/trk/register_default.ts"
+    },
     "#datasource/vtk/backend": {
       "neuroglancer/datasource/vtk:enabled": "./src/datasource/vtk/backend.ts",
       "neuroglancer/datasource:none_by_default": "./src/util/false.ts",

src/datasource/enabled_async_computation_modules.ts

@@ -9,5 +9,6 @@ import "#datasource/nifti/async_computation";
 import "#datasource/obj/async_computation";
 import "#datasource/precomputed/async_computation";
 import "#datasource/render/async_computation";
+import "#datasource/trk/async_computation";
 import "#datasource/vtk/async_computation";
 import "#datasource/zarr/async_computation";

src/datasource/enabled_backend_modules.ts

@@ -11,5 +11,6 @@ import "#datasource/obj/backend";
 import "#datasource/precomputed/backend";
 import "#datasource/python/backend";
 import "#datasource/render/backend";
+import "#datasource/trk/backend";
 import "#datasource/vtk/backend";
 import "#datasource/zarr/backend";

src/datasource/enabled_frontend_modules.ts

@@ -15,5 +15,6 @@ import "#datasource/nifti/register_default";
 import "#datasource/obj/register_default";
 import "#datasource/precomputed/register_default";
 import "#datasource/render/register_default";
+import "#datasource/trk/register_default";
 import "#datasource/vtk/register_default";
 import "#datasource/zarr/register_default";

src/datasource/trk/backend.ts

@@ -0,0 +1,48 @@
+/**
+ * @license
+ * Copyright 2016 Google Inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+import { WithParameters } from "#src/chunk_manager/backend.js";
+import { WithSharedCredentialsProviderCounterpart } from "#src/credentials_provider/shared_counterpart.js";
+import {
+    SkeletonSourceParameters,
+} from "#src/datasource/trk/base.js";
+import type { SkeletonChunk } from "#src/skeleton/backend.js";
+import { SkeletonSource } from "#src/skeleton/backend.js";
+import { decodeSkeletonChunk } from "#src/skeleton/decode_precomputed_skeleton.js";
+import type {
+    SpecialProtocolCredentials,
+} from "#src/util/special_protocol_request.js";
+import { registerSharedObject } from "#src/worker_rpc.js";
+
+
+console.log(import.meta.url);
+
+@registerSharedObject()
+export class trkSkeletonSource extends WithParameters(
+    WithSharedCredentialsProviderCounterpart<SpecialProtocolCredentials>()(
+        SkeletonSource,
+    ),
+    SkeletonSourceParameters,
+) {
+    async download(chunk: SkeletonChunk,
+    ) {
+        const { parameters } = this;
+
+        decodeSkeletonChunk(chunk, parameters.skeletonBuffer, parameters.metadata.vertexAttributes);
+    }
+}
+

src/datasource/trk/base.ts

@@ -0,0 +1,41 @@
+/**
+ * @license
+ * Copyright 2016 Google Inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import type { VertexAttributeInfo } from "#src/skeleton/base.js";
+import type { mat4 } from "#src/util/geom.js";
+
+
+export enum DataEncoding {
+  RAW = 0,
+  GZIP = 1,
+}
+
+export enum ShardingHashFunction {
+  IDENTITY = 0,
+  MURMURHASH3_X86_128 = 1,
+}
+
+export interface SkeletonMetadata {
+  transform: mat4;
+  vertexAttributes: Map<string, VertexAttributeInfo>;
+}
+
+export class SkeletonSourceParameters {
+  url: string;
+  metadata: SkeletonMetadata;
+  skeletonBuffer: ArrayBuffer;
+  static RPC_ID = "trk/SkeletonSource";
+}