Fix parsing failure during import of ngff zarr datasets with translat…

…ion transforms (#6621)
scalableminds · Nov 10, 2022 · 35c3673 · 35c3673
1 parent b18635a
commit 35c3673
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Showing 3 changed files with 9 additions and 7 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -29,6 +29,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - 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)
 
 ### Removed
 

diff --git a/app/models/binary/explore/NgffExplorer.scala b/app/models/binary/explore/NgffExplorer.scala
@@ -148,9 +148,10 @@ class NgffExplorer extends RemoteLayerExplorer {
   private def extractAndCombineScaleTransforms(coordinateTransforms: List[NgffCoordinateTransformation],
                                                axisOrder: AxisOrder): Vec3Double = {
     val filtered = coordinateTransforms.filter(_.`type` == "scale")
-    val xFactors = filtered.map(_.scale(axisOrder.x))
-    val yFactors = filtered.map(_.scale(axisOrder.y))
-    val zFactors = filtered.map(_.scale(axisOrder.z))
+    val scalesFromTransforms = filtered.flatMap(_.scale)
+    val xFactors = scalesFromTransforms.map(_(axisOrder.x))
+    val yFactors = scalesFromTransforms.map(_(axisOrder.y))
+    val zFactors = scalesFromTransforms.map(_(axisOrder.z))
     Vec3Double(xFactors.product, yFactors.product, zFactors.product)
   }
 }
diff --git a/...-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadata.scala b/...-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadata.scala
@@ -6,7 +6,7 @@ import play.api.libs.json.{Json, OFormat}
 
 import scala.concurrent.ExecutionContext
 
-case class NgffCoordinateTransformation(`type`: String = "scale", scale: List[Double])
+case class NgffCoordinateTransformation(`type`: String = "scale", scale: Option[List[Double]])
 
 object NgffCoordinateTransformation {
   implicit val jsonFormat: OFormat[NgffCoordinateTransformation] = Json.format[NgffCoordinateTransformation]
@@ -90,9 +90,9 @@ object NgffMetadata {
   def fromNameScaleAndMags(dataLayerName: String, dataSourceScale: Vec3Double, mags: List[Vec3Int]): NgffMetadata = {
     val datasets = mags.map(
       mag =>
-        NgffDataset(
-          path = mag.toMagLiteral(allowScalar = true),
-          List(NgffCoordinateTransformation(scale = List[Double](1.0) ++ (dataSourceScale * Vec3Double(mag)).toList))))
+        NgffDataset(path = mag.toMagLiteral(allowScalar = true),
+                    List(NgffCoordinateTransformation(
+                      scale = Some(List[Double](1.0) ++ (dataSourceScale * Vec3Double(mag)).toList)))))
     NgffMetadata(multiscales = List(NgffMultiscalesItem(name = Some(dataLayerName), datasets = datasets)))
   }