Move 'axes' logic to ome.ts

hms-dbmi · Aug 5, 2021 · 8ed9c89 · 8ed9c89
1 parent 3617cb8
commit 8ed9c89
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Showing 2 changed files with 10 additions and 9 deletions.
diff --git a/src/io.ts b/src/io.ts
@@ -110,9 +110,6 @@ export async function createSourceData(config: ImageLayerConfig): Promise<Source
 
   if (node instanceof ZarrGroup) {
     const attrs = (await node.attrs.asObject()) as Ome.Attrs;
-    if ('multiscales' in attrs && attrs.multiscales?.[0]?.axes) {
-      config.axis_labels = attrs.multiscales?.[0]?.axes;
-    }
 
     if ('plate' in attrs) {
       return loadPlate(config, node, attrs.plate);

diff --git a/src/ome.ts b/src/ome.ts
@@ -51,7 +51,7 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
   // Create loader for every Image.
   const promises = imgPaths.map((p) => grp.getItem(join(p, resolution)));
   const data = (await Promise.all(promises)) as ZarrArray[];
-  const axis_labels = getOmeAxisLabels(config.axis_labels);
+  const axis_labels = getOmeAxisLabels(imgAttrs);
   const meta = parseOmeroMeta(imgAttrs.omero, axis_labels);
 
   const tileSize = guessTileSize(data[0]);
@@ -141,7 +141,7 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
     { concurrency: 10 }
   );
   const data = await Promise.all(promises);
-  const axis_labels = getOmeAxisLabels(imgAttrs.multiscales[0].axes || config.axis_labels);
+  const axis_labels = getOmeAxisLabels(imgAttrs);
   const meta = parseOmeroMeta(imgAttrs.omero, axis_labels);
   const tileSize = guessTileSize(data[0][1]);
   const loaders = data.map((d) => {
@@ -200,7 +200,7 @@ export async function loadOmeroMultiscales(
 ): Promise<SourceData> {
   const { name, opacity = 1, colormap = '' } = config;
   const data = await loadMultiscales(grp, attrs.multiscales);
-  const axis_labels = getOmeAxisLabels(config.axis_labels);
+  const axis_labels = getOmeAxisLabels(attrs);
   const meta = parseOmeroMeta(attrs.omero, axis_labels);
   const tileSize = guessTileSize(data[0]);
 
@@ -247,12 +247,16 @@ function parseOmeroMeta({ rdefs, channels, name }: Ome.Omero, axis_labels: strin
     colors,
     contrast_limits,
     visibilities,
-    channel_axis: axis_labels.includes('c') ? axis_labels.indexOf('c') : undefined,
+    channel_axis: axis_labels.includes('c') ? axis_labels.indexOf('c') : null,
     defaultSelection,
   };
 }
 
-function getOmeAxisLabels(axes?: string[]): [...string[], 'y', 'x'] {
+function getOmeAxisLabels(attrs: Ome.Attrs): [...string[], 'y', 'x'] {
+  let axis_labels;
+  if ('multiscales' in attrs && attrs.multiscales?.[0]?.axes) {
+    axis_labels = attrs.multiscales[0].axes;
+  }
   const default_axes = ['t', 'c', 'z', 'y', 'x']; // v0.1 & v0.2
-  return (axes || default_axes) as [...string[], 'y', 'x'];
+  return (axis_labels || default_axes) as [...string[], 'y', 'x'];
 }