Merge branch 'master' of github.com:scalableminds/webknossos into ci

scalableminds · Oct 21, 2024 · 5cb454b · 5cb454b
2 parents e401934 + fb9b450
commit 5cb454b
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 9 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -25,6 +25,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug during dataset upload in case the configured `datastore.baseFolder` is an absolute path. [#8098](https://github.com/scalableminds/webknossos/pull/8098) [#8103](https://github.com/scalableminds/webknossos/pull/8103)
 - Fixed that the skeleton search did not automatically expand groups that contained the selected tree [#8129](https://github.com/scalableminds/webknossos/pull/8129)
 - Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. [#8116](https://github.com/scalableminds/webknossos/pull/8116)
+- Fixed sorting of mags in outbound zarr streaming. [#8125](https://github.com/scalableminds/webknossos/pull/8125)
 - Fixed a bug where you could not create annotations for public datasets of other organizations. [#8107](https://github.com/scalableminds/webknossos/pull/8107)
 - Users without edit permissions to a dataset can no longer delete sharing tokens via the API. [#8083](https://github.com/scalableminds/webknossos/issues/8083)
 

diff --git a/...tore/app/com/scalableminds/webknossos/datastore/controllers/ZarrStreamingController.scala b/...tore/app/com/scalableminds/webknossos/datastore/controllers/ZarrStreamingController.scala
@@ -62,7 +62,7 @@ class ZarrStreamingController @Inject()(
                                                                                   datasetName,
                                                                                   dataLayerName) ?~> Messages(
           "dataSource.notFound") ~> NOT_FOUND
-        omeNgffHeader = NgffMetadata.fromNameVoxelSizeAndMags(dataLayerName, dataSource.scale, dataLayer.resolutions)
+        omeNgffHeader = NgffMetadata.fromNameVoxelSizeAndMags(dataLayerName, dataSource.scale, dataLayer.sortedMags)
       } yield Ok(Json.toJson(omeNgffHeader))
     }
   }
@@ -82,7 +82,7 @@ class ZarrStreamingController @Inject()(
           "dataSource.notFound") ~> NOT_FOUND
         omeNgffHeaderV0_5 = NgffMetadataV0_5.fromNameVoxelSizeAndMags(dataLayerName,
                                                                       dataSource.scale,
-                                                                      dataLayer.resolutions,
+                                                                      dataLayer.sortedMags,
                                                                       dataLayer.additionalAxes)
         zarr3GroupHeader = Zarr3GroupHeader(3, "group", Some(omeNgffHeaderV0_5))
       } yield Ok(Json.toJson(zarr3GroupHeader))
@@ -110,7 +110,7 @@ class ZarrStreamingController @Inject()(
               "dataSource.notFound") ~> NOT_FOUND
             dataSourceOmeNgffHeader = NgffMetadata.fromNameVoxelSizeAndMags(dataLayerName,
                                                                             dataSource.scale,
-                                                                            dataLayer.resolutions)
+                                                                            dataLayer.sortedMags)
           } yield Ok(Json.toJson(dataSourceOmeNgffHeader))
       )
     }
@@ -136,7 +136,7 @@ class ZarrStreamingController @Inject()(
               "dataSource.notFound") ~> NOT_FOUND
             dataSourceOmeNgffHeader = NgffMetadataV0_5.fromNameVoxelSizeAndMags(dataLayerName,
                                                                                 dataSource.scale,
-                                                                                dataLayer.resolutions,
+                                                                                dataLayer.sortedMags,
                                                                                 dataLayer.additionalAxes)
             zarr3GroupHeader = Zarr3GroupHeader(3, "group", Some(dataSourceOmeNgffHeader))
           } yield Ok(Json.toJson(zarr3GroupHeader))
@@ -173,7 +173,7 @@ class ZarrStreamingController @Inject()(
           s.name,
           s.boundingBox,
           s.elementClass,
-          mags = s.resolutions.map(x => MagLocator(x, None, None, Some(AxisOrder.cAdditionalxyz(rank)), None, None)),
+          mags = s.sortedMags.map(x => MagLocator(x, None, None, Some(AxisOrder.cAdditionalxyz(rank)), None, None)),
           mappings = s.mappings,
           largestSegmentId = s.largestSegmentId,
           numChannels = Some(if (s.elementClass == ElementClass.uint24) 3 else 1),
@@ -190,7 +190,7 @@ class ZarrStreamingController @Inject()(
           d.category,
           d.boundingBox,
           d.elementClass,
-          mags = d.resolutions.map(x => MagLocator(x, None, None, Some(AxisOrder.cAdditionalxyz(rank)), None, None)),
+          mags = d.sortedMags.map(x => MagLocator(x, None, None, Some(AxisOrder.cAdditionalxyz(rank)), None, None)),
           numChannels = Some(if (d.elementClass == ElementClass.uint24) 3 else 1),
           defaultViewConfiguration = d.defaultViewConfiguration,
           adminViewConfiguration = d.adminViewConfiguration,
@@ -480,7 +480,7 @@ class ZarrStreamingController @Inject()(
     for {
       (_, dataLayer) <- dataSourceRepository.getDataSourceAndDataLayer(organizationId, datasetName, dataLayerName) ?~> Messages(
         "dataSource.notFound") ~> NOT_FOUND
-      mags = dataLayer.resolutions
+      mags = dataLayer.sortedMags
       additionalFiles = if (zarrVersion == 2)
         List(NgffMetadata.FILENAME_DOT_ZATTRS, NgffGroupHeader.FILENAME_DOT_ZGROUP)
       else List(Zarr3ArrayHeader.FILENAME_ZARR_JSON)

diff --git a/...os-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataLayer.scala b/...os-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataLayer.scala
@@ -148,6 +148,8 @@ trait DataLayerLike {
 
   def resolutions: List[Vec3Int]
 
+  lazy val sortedMags: List[Vec3Int] = resolutions.sortBy(_.maxDim)
+
   def elementClass: ElementClass.Value
 
   // This is the default from the DataSource JSON.

diff --git a/...lableminds/webknossos/tracingstore/controllers/VolumeTracingZarrStreamingController.scala b/...lableminds/webknossos/tracingstore/controllers/VolumeTracingZarrStreamingController.scala
@@ -247,11 +247,11 @@ class VolumeTracingZarrStreamingController @Inject()(
       for {
         tracing <- tracingService.find(tracingId) ?~> Messages("tracing.notFound") ~> NOT_FOUND
 
-        existingMags = tracing.resolutions.map(vec3IntFromProto)
+        sortedExistingMags = tracing.resolutions.map(vec3IntFromProto).toList.sortBy(_.maxDim)
         dataSource <- remoteWebknossosClient.getDataSourceForTracing(tracingId) ~> NOT_FOUND
         omeNgffHeader = NgffMetadataV0_5.fromNameVoxelSizeAndMags(tracingId,
                                                                   dataSourceVoxelSize = dataSource.scale,
-                                                                  mags = existingMags.toList,
+                                                                  mags = sortedExistingMags,
                                                                   additionalAxes = dataSource.additionalAxesUnion)
         zarr3GroupHeader = Zarr3GroupHeader(3, "group", Some(omeNgffHeader))
       } yield Ok(Json.toJson(zarr3GroupHeader))