Cleanup and use schema from ome branch on NGFF repo

ome · Oct 25, 2024 · 775c3d2 · 775c3d2
1 parent 6acf3b2
commit 775c3d2
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Showing 9 changed files with 9 additions and 15 deletions.
diff --git a/public/ngff_viewers.json b/public/ngff_viewers.json
@@ -14,7 +14,7 @@
       "name": "neuroglancer",
       "logo": "/neuroglancer.png",
       "//": "NB: The {URL} in the href is replaced with NGFF image URL",
-      "href": "https://neuroglancer-demo.appspot.com/#!{%22layers%22:[{%22source%22:%22zarr3://{URL}%22,%22name%22:%22OME-NGFF%22}]}"
+      "href": "https://neuroglancer-demo.appspot.com/#!{%22layers%22:[{%22source%22:%22zarr://{URL}%22,%22name%22:%22OME-NGFF%22}]}"
     },
     {
       "name": "Allen Cell Feature Explorer 3D viewer",

diff --git a/src/Bioformats2rawLayout/index.svelte b/src/Bioformats2rawLayout/index.svelte
@@ -49,7 +49,7 @@
       // MUST match if we have both...
       if (series.length !== xmlRsp.images.length) {
         rsp.errors = [
-          `Length mismatch: series: ${series.length} != ome.xml: ${5}`,
+          `Images length mismatch: series: ${series.length} != ome.xml: ${xmlRsp.images.length}`,
         ];
       }
     }
@@ -109,7 +109,7 @@
 </script>
 
 <article>
-  Reading: <a href={source}>/{zarrName}/{zarrAttrsFileName}</a>
+  Reading: <a href={source}/{zarrAttrsFileName}>/{zarrName}/{zarrAttrsFileName}</a>
 
   Loading metadata:<a href={metadataUrl}>{metadataName}</a><br />
 

diff --git a/src/JsonBrowser/DetailsPrePanel.svelte b/src/JsonBrowser/DetailsPrePanel.svelte
@@ -28,4 +28,4 @@ details {
     overflow: auto;
   }
 
-</style>
+</style>
diff --git a/src/JsonValidator/MultiscaleArrays/ZarrArray/ChunkLoader.svelte b/src/JsonValidator/MultiscaleArrays/ZarrArray/ChunkLoader.svelte
@@ -1,5 +1,4 @@
 <script>
-  // import { openArray, slice } from "zarr";
   import { range, getChunkAndShardShapes } from "../../../utils";
   import { get, writable } from "svelte/store";
   import ChunkViewer from "./ChunkViewer.svelte";
@@ -40,8 +39,6 @@
     // clear previous chunk
     chunk = undefined;
 
-    // Use zarr like this, otherwise we get "Error: Unknown codec: bytes"
-    // let zarr = await import("https://cdn.jsdelivr.net/npm/zarrita@next/+esm");
     let url = source + "/" + zarrPath;
     const store = new zarr.FetchStore(url);
     const arr = await zarr.open(store, { kind: "array" });

diff --git a/src/JsonValidator/MultiscaleArrays/ZarrArray/ChunkViewer.svelte b/src/JsonValidator/MultiscaleArrays/ZarrArray/ChunkViewer.svelte
@@ -92,7 +92,6 @@
       try {
         console.log('renderImageToCanvas...', chunk.shape)
         chunk2d = sliceArray(chunk, chunkSlice);
-        // chunk2d = chunk;
         errorMsg = undefined;
       } catch (error) {
         errorMsg = `Slicing (${chunk.shape}) failed with slice (${chunkSlice})`;

diff --git a/src/JsonValidator/RoCrate/RoCrateValidator.svelte b/src/JsonValidator/RoCrate/RoCrateValidator.svelte
@@ -4,7 +4,7 @@
 
     export let jsonData;
 
-    // Try to find various fields in the Ro-Crate metadata
+    // Try to find various fields in the RO-Crate metadata
     let license = jsonData["@graph"].find(item => item["license"])?.license;
     let name = jsonData["@graph"].find(item => item["name"])?.name;
     let description = jsonData["@graph"].find(item => item["description"])?.description;

diff --git a/src/JsonValidator/RoCrate/index.svelte b/src/JsonValidator/RoCrate/index.svelte
@@ -37,4 +37,4 @@
     background: linear-gradient(to right, #ccc, #aaa);
     text-align: center;
 }
-</style>
+</style>
diff --git a/src/JsonValidator/index.svelte b/src/JsonValidator/index.svelte
@@ -63,7 +63,7 @@
 
 <article>
   <p>
-    Validating: <a href={source}>/{zarrName}/{zarrAttrsFileName}</a>
+    Validating: <a href={source}/{zarrAttrsFileName}>/{zarrName}/{zarrAttrsFileName}</a>
   </p>
 
   {versionMessage}

diff --git a/src/utils.js b/src/utils.js
@@ -8,10 +8,8 @@ export const FILE_NOT_FOUND = "File not found";
 
 export function getSchemaUrl(schemaName, version) {
   if (version == "0.5" || version == "0.5-dev2") {
-    // TEMP: use open PR branch
-    return `https://raw.githubusercontent.com/normanrz/ngff/spec-rfc2/latest/schemas/${schemaName}.schema`;
-  } else if (version == "0.5-dev1") {
-    return `https://raw.githubusercontent.com/d-v-b/ngff/multiple_zarr_versions/0.5-dev1/schemas/${schemaName}.schema`;
+    // TEMP: use our branch based on Norman's spec-rfc2 PR at https://github.com/ome/ngff/pull/242
+    return `https://raw.githubusercontent.com/ome/ngff/spec-rfc2/latest/schemas/${schemaName}.schema`;
   }
   return `https://raw.githubusercontent.com/ome/ngff/main/${version}/schemas/${schemaName}.schema`;
 }