Fix NGFF import for datasets with no channel axis (#6637)

scalableminds · Nov 12, 2022 · f3d6f07 · f3d6f07
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -30,6 +30,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed importing a dataset from disk. [#6615](https://github.com/scalableminds/webknossos/pull/6615)
 - Fixed a bug in the dataset import view, where the layer name text field would lose focus after each key press. [#6615](https://github.com/scalableminds/webknossos/pull/6615)
 - Fixed importing NGFF Zarr datasets with non-scale transforms. [#6621](https://github.com/scalableminds/webknossos/pull/6621)
+- Fixed a regression in NGFF Zarr import for datasets with no channel axis. [#6636](https://github.com/scalableminds/webknossos/pull/6636)
 
 ### Removed
 

diff --git a/app/models/binary/explore/NgffExplorer.scala b/app/models/binary/explore/NgffExplorer.scala
@@ -42,8 +42,11 @@ class NgffExplorer extends RemoteLayerExplorer {
       zarrayPath = magPath.resolve(ZarrHeader.FILENAME_DOT_ZARRAY)
       zarrHeader <- parseJsonFromPath[ZarrHeader](zarrayPath) ?~> s"failed to read zarr header at $zarrayPath"
       axisOrder <- extractAxisOrder(multiscale.axes) ?~> "Could not extract XYZ axis order mapping. Does the data have x, y and z axes, stated in multiscales metadata?"
-      channelAxisIndex <- axisOrder.c.toFox
-    } yield zarrHeader.shape(channelAxisIndex)
+      channelCount = axisOrder.c match {
+        case Some(channeAxislIndex) => zarrHeader.shape(channeAxislIndex)
+        case _                      => 1
+      }
+    } yield channelCount
 
   private def layersFromNgffMultiscale(multiscale: NgffMultiscalesItem,
                                        remotePath: Path,