@aics/vole-core 4.4.1 → 4.5.0

package/es/loaders/JsonImageInfoLoader.js

@@ -3,6 +3,7 @@ import { ThreadableVolumeLoader } from "./IVolumeLoader.js";
 import { computeAtlasSize } from "../ImageInfo.js";
 import { isChunk } from "../VolumeCache.js";
 import { getDataRange } from "../utils/num_utils.js";
+import { remapUri } from "../utils/url_utils.js";
 
 /* eslint-disable @typescript-eslint/naming-convention */
 
@@ -70,7 +71,7 @@ class JsonImageInfoLoader extends ThreadableVolumeLoader {
     if (cachedInfo) {
       return cachedInfo;
     }
-    const response = await fetch(this.urls[time]);
+    const response = await fetch(remapUri(this.urls[time]));
     const imageInfo = await response.json();
     imageInfo.pixel_size_unit = imageInfo.pixel_size_unit || "μm";
     imageInfo.times = imageInfo.times || this.urls.length;
@@ -194,7 +195,7 @@ class JsonImageInfoLoader extends ThreadableVolumeLoader {
       if (cacheHit) {
         return;
       }
-      const response = await fetch(image.name, {
+      const response = await fetch(remapUri(image.name), {
         mode: "cors"
       });
       const blob = await response.blob();

package/es/loaders/OmeZarrLoader.js

@@ -12,6 +12,7 @@ import { getScale, getSourceChannelMeta, matchSourceScaleLevels, orderByDimensio
 import { VolumeLoadError, VolumeLoadErrorType, wrapVolumeLoadError } from "./VolumeLoadError.js";
 import wrapArray, { RelaxedFetchStore } from "./zarr_utils/wrappers.js";
 import { assertMetadataHasMultiscales, toOMEZarrMetaV4, validateOMEZarrMetadata } from "./zarr_utils/validation.js";
+import { remapUri } from "../utils/url_utils.js";
 const CHUNK_REQUEST_CANCEL_REASON = "chunk request cancelled";
 
 // returns the converted data and the original min and max values
@@ -81,7 +82,7 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
     if (!queue) {
       queue = new SubscribableRequestQueue(fetchOptions?.concurrencyLimit, fetchOptions?.prefetchConcurrencyLimit);
     }
-    const urlsArr = Array.isArray(urls) ? urls : [urls];
+    const urlsArr = (Array.isArray(urls) ? urls : [urls]).map(remapUri);
     const scenesArr = Array.isArray(scenes) ? scenes : [scenes];
 
     // Create one `ZarrSource` per URL

package/es/loaders/TiffLoader.js

@@ -4,6 +4,7 @@ import { ThreadableVolumeLoader, LoadSpec } from "./IVolumeLoader.js";
 import { computePackedAtlasDims, MAX_ATLAS_EDGE } from "./VolumeLoaderUtils.js";
 import { VolumeLoadError, VolumeLoadErrorType, wrapVolumeLoadError } from "./VolumeLoadError.js";
 import { CImageInfo } from "../ImageInfo.js";
+import { remapUri } from "../utils/url_utils.js";
 function trimNull(xml) {
   // trim trailing unicode zeros?
   return xml && xml.trim().replace(/\0/g, "").trim();
@@ -92,7 +93,7 @@ const getPixelType = pxSize => pxSize === 1 ? "uint8" : pxSize === 2 ? "uint16"
 class TiffLoader extends ThreadableVolumeLoader {
   constructor(url) {
     super();
-    this.url = url;
+    this.url = url.map(remapUri);
   }
   async loadOmeDims() {
     if (!this.dims) {

package/es/types/loaders/TiffLoader.d.ts

@@ -35,7 +35,7 @@ export type TiffLoadResult = {
     range: [number, number];
 };
 declare class TiffLoader extends ThreadableVolumeLoader {
-    url: string[];
+    private url;
     dims?: OMEDims;
     constructor(url: string[]);
     private loadOmeDims;

package/es/types/utils/url_utils.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Remaps non-standard URIs (e.g. S3 (`s3://`), Google Cloud Storage (`gs://`), or
+ * VAST files (`/allen/aics/`)) to a standard HTTPS URL.
+ */
+export declare function remapUri(url: string): string;

package/es/utils/url_utils.js

@@ -0,0 +1,25 @@
+const S3_URL_PREFIX = "s3://";
+const GCS_URL_PREFIX = "gs://";
+const VAST_FILES_PREFIX = "/allen/aics/";
+const VAST_FILES_URL = "https://vast-files.int.allencell.org/";
+
+/**
+ * Remaps non-standard URIs (e.g. S3 (`s3://`), Google Cloud Storage (`gs://`), or
+ * VAST files (`/allen/aics/`)) to a standard HTTPS URL.
+ */
+export function remapUri(url) {
+  let newUrl = url.trim();
+  if (newUrl.startsWith(S3_URL_PREFIX)) {
+    // remap s3://bucket/key to https://bucket.s3.amazonaws.com/key
+    const s3Path = newUrl.slice(S3_URL_PREFIX.length);
+    const pathSegments = s3Path.split("/");
+    newUrl = `https://${pathSegments[0]}.s3.amazonaws.com/${pathSegments.slice(1).join("/")}`;
+  } else if (newUrl.startsWith(GCS_URL_PREFIX)) {
+    // remap gs://bucket/key to https://storage.googleapis.com/bucket/key
+    newUrl = newUrl.replace(GCS_URL_PREFIX, "https://storage.googleapis.com/");
+  } else if (newUrl.startsWith(VAST_FILES_PREFIX)) {
+    // remap /allen/aics/... to https://vast-files.int.allencell.org/...
+    newUrl = newUrl.replace(VAST_FILES_PREFIX, VAST_FILES_URL);
+  }
+  return newUrl;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "4.4.1",
+  "version": "4.5.0",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",