fix(loaders): Allow optional TiffData in OME-XML (#714)

hms-dbmi · Nov 14, 2023 · 2198e50 · 2198e50
1 parent b56f4ad
commit 2198e50
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Showing 3 changed files with 17 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 ### Changed
 - Fix Avivator demo for OME-Zarr with only spatial axes
+- Allow OME-XML to omit `TiffData` tags
 
 ## 0.14.1
 

diff --git a/packages/loaders/src/omexml.ts b/packages/loaders/src/omexml.ts
@@ -114,7 +114,7 @@ const TiffDataSchema = z
 const PixelsSchema = z
   .object({
     Channel: z.preprocess(ensureArray, ChannelSchema.array()),
-    TiffData: z.preprocess(ensureArray, TiffDataSchema.array())
+    TiffData: z.preprocess(ensureArray, TiffDataSchema.array()).optional()
   })
   .extend({
     attr: z.object({

diff --git a/sites/avivator/src/utils.js b/sites/avivator/src/utils.js
@@ -135,6 +135,14 @@ async function getTotalImageCount(src, rootMeta, data) {
   return numImagesPerResolution * levels;
 }
 
+/**
+ * @param {unknown} e
+ * @returns {e is Error & { issues: unknown }}
+ */
+function isZodError(e) {
+  return e instanceof Error && 'issues' in e;
+}
+
 /**
  * Given an image source, creates a PixelSource[] and returns XML-meta
  *
@@ -211,7 +219,13 @@ export async function createLoader(
     let source;
     try {
       source = await loadBioformatsZarr(urlOrFile);
-    } catch {
+    } catch (e) {
+      if (isZodError(e)) {
+        // If the error is a ZodError, it means there was an OME-XML file
+        // but it was invalid. We shouldn't try to load the file as a OME-Zarr.
+        throw e;
+      }
+
       // try ome-zarr
       const res = await loadOmeZarr(urlOrFile, { type: 'multiscales' });
       // extract metadata into OME-XML-like form