Ome ngff volume annotation (#6242)

* add routes for zattrs for volume annotations * get data source for tracing to extract scale * add changelog entry * reformat
scalableminds · May 26, 2022 · 7453c97 · 7453c97
1 parent 77775e4
commit 7453c97
Show file tree

Hide file tree

Showing 5 changed files with 56 additions and 20 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -21,6 +21,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Adding a New Volume Layer via the left border tab now gives the option to restrict resolutions for the new layer. [#6229](https://github.com/scalableminds/webknossos/pull/6229)
 - Added support for segment interpolation with depths > 2. Also, the feature was changed to work on an explicit trigger (either via the button in the toolbar or via the shortcut V). When triggering the interpolation, the current segment id is interpolated between the current slice and the least-recently annotated slice. [#6235](https://github.com/scalableminds/webknossos/pull/6235)
 - Added Route to get OME-NGFF Headers for a data layer (.zattrs file) following the corresponding [spec](https://ngff.openmicroscopy.org/latest/). [#6226](https://github.com/scalableminds/webknossos/pull/6226)
+- Added Route to get OME-NGFF Headers for Volume annotation. [#6242](https://github.com/scalableminds/webknossos/pull/6242)
 
 ### Changed
 - When creating a new annotation with a volume layer (without fallback) for a dataset which has an existing segmentation layer, the original segmentation layer is still listed (and viewable) in the left sidebar. Earlier versions simply hid the original segmentation layer. [#6186](https://github.com/scalableminds/webknossos/pull/6186)

diff --git a/...tore/app/com/scalableminds/webknossos/datastore/controllers/ZarrStreamingController.scala b/...tore/app/com/scalableminds/webknossos/datastore/controllers/ZarrStreamingController.scala
@@ -174,9 +174,9 @@ class ZarrStreamingController @Inject()(
           "dataSource.notFound") ~> 404
         existingMags = dataLayer.resolutions
 
-        omeNgffHeader = OmeNgffHeader.createFromDataLayerName(dataLayerName,
-                                                              dataSourceScale = dataSource.scale,
-                                                              mags = existingMags)
+        omeNgffHeader = OmeNgffHeader.fromDataLayerName(dataLayerName,
+                                                        dataSourceScale = dataSource.scale,
+                                                        mags = existingMags)
       } yield Ok(Json.toJson(omeNgffHeader))
     }
   }

diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/jzarr/OmeNgffHeader.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/jzarr/OmeNgffHeader.scala
@@ -40,9 +40,7 @@ object OmeNgffOneHeader {
 case class OmeNgffHeader(multiscales: List[OmeNgffOneHeader])
 
 object OmeNgffHeader {
-  def createFromDataLayerName(dataLayerName: String,
-                              dataSourceScale: Vec3Double,
-                              mags: List[Vec3Int]): OmeNgffHeader = {
+  def fromDataLayerName(dataLayerName: String, dataSourceScale: Vec3Double, mags: List[Vec3Int]): OmeNgffHeader = {
     val datasets = mags.map(
       mag =>
         OmeNgffDataset(

diff --git a/...e/app/com/scalableminds/webknossos/tracingstore/controllers/VolumeTracingController.scala b/...e/app/com/scalableminds/webknossos/tracingstore/controllers/VolumeTracingController.scala
@@ -7,15 +7,16 @@ import java.io.File
 import java.nio.{ByteBuffer, ByteOrder}
 import akka.stream.scaladsl.Source
 import com.google.inject.Inject
-import com.scalableminds.util.geometry.{BoundingBox, Vec3Int}
+import com.scalableminds.util.geometry.{BoundingBox, Vec3Double, Vec3Int}
 import com.scalableminds.util.tools.ExtendedTypes.ExtendedString
 import com.scalableminds.util.tools.Fox
-import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, ElementClass}
+import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
 import com.scalableminds.webknossos.datastore.models.{WebKnossosDataRequest, WebKnossosIsosurfaceRequest}
 import com.scalableminds.webknossos.datastore.services.UserAccessRequest
 import com.scalableminds.webknossos.datastore.VolumeTracing.{VolumeTracing, VolumeTracingOpt, VolumeTracings}
 import com.scalableminds.webknossos.datastore.dataformats.zarr.ZarrCoordinatesParser
 import com.scalableminds.webknossos.datastore.helpers.ProtoGeometryImplicits
+import com.scalableminds.webknossos.datastore.jzarr.{ArrayOrder, OmeNgffHeader, ZarrHeader}
 import com.scalableminds.webknossos.datastore.rpc.RPC
 import com.scalableminds.webknossos.tracingstore.slacknotification.TSSlackNotificationService
 import com.scalableminds.webknossos.tracingstore.tracings.volume.{ResolutionRestrictions, VolumeTracingService}
@@ -270,24 +271,36 @@ class VolumeTracingController @Inject()(
           (channels, dtype) = ElementClass.toChannelAndZarrString(tracing.elementClass)
           // data request method always decompresses before sending
           compressor = None
+
+          shape = Array(
+            channels,
+            // Zarr can't handle data sets that don't start at 0, so we extend shape to include "true" coords
+            (tracing.boundingBox.width + tracing.boundingBox.topLeft.x) / magParsed.x,
+            (tracing.boundingBox.height + tracing.boundingBox.topLeft.y) / magParsed.y,
+            (tracing.boundingBox.depth + tracing.boundingBox.topLeft.z) / magParsed.z
+          )
+
+          chunks = Array(channels, cubeLength, cubeLength, cubeLength)
+
+          zarrHeader = ZarrHeader(zarr_format = 2,
+                                  shape = shape,
+                                  chunks = chunks,
+                                  compressor = compressor,
+                                  dtype = dtype,
+                                  order = ArrayOrder.F)
         } yield
           Ok(
+            // Json.toJson doesn't work on zarrHeader at the moment, because it doesn't write None values in Options
             Json.obj(
-              "dtype" -> dtype,
+              "dtype" -> zarrHeader.dtype,
               "fill_value" -> 0,
-              "zarr_format" -> 2,
-              "order" -> "F",
-              "chunks" -> List(channels, cubeLength, cubeLength, cubeLength),
+              "zarr_format" -> zarrHeader.zarr_format,
+              "order" -> zarrHeader.order,
+              "chunks" -> zarrHeader.chunks,
               "compressor" -> compressor,
               "filters" -> None,
-              "shape" -> List(
-                channels,
-                // Zarr can't handle data sets that don't start at 0, so we extend shape to include "true" coords
-                (tracing.boundingBox.width + tracing.boundingBox.topLeft.x) / magParsed.x,
-                (tracing.boundingBox.height + tracing.boundingBox.topLeft.y) / magParsed.y,
-                (tracing.boundingBox.depth + tracing.boundingBox.topLeft.z) / magParsed.z
-              ),
-              "dimension_seperator" -> "."
+              "shape" -> zarrHeader.shape,
+              "dimension_seperator" -> zarrHeader.dimension_separator
             ))
       }
   }
@@ -298,6 +311,29 @@ class VolumeTracingController @Inject()(
     }
   }
 
+  /**
+    * Handles a request for .zattrs file for a Volume Tracing via a HTTP GET.
+    * Uses the OME-NGFF standard (see https://ngff.openmicroscopy.org/latest/)
+    * Used by zarr-streaming.
+    */
+  def zAttrs(
+      token: Option[String],
+      tracingId: String,
+  ): Action[AnyContent] = Action.async { implicit request =>
+    accessTokenService.validateAccess(UserAccessRequest.readTracing(tracingId), urlOrHeaderToken(token, request)) {
+      for {
+        tracing <- tracingService.find(tracingId) ?~> Messages("tracing.notFound")
+
+        existingMags = tracing.resolutions.map(vec3IntFromProto)
+        dataSource <- remoteWebKnossosClient.getDataSource(tracing.organizationName, tracing.dataSetName)
+
+        omeNgffHeader = OmeNgffHeader.fromDataLayerName(tracingId,
+                                                        dataSourceScale = dataSource.scale,
+                                                        mags = existingMags.toList)
+      } yield Ok(Json.toJson(omeNgffHeader))
+    }
+  }
+
   def rawZarrCube(token: Option[String], tracingId: String, mag: String, cxyz: String): Action[AnyContent] =
     Action.async { implicit request =>
       {

diff --git a/webknossos-tracingstore/conf/com.scalableminds.webknossos.tracingstore.routes b/webknossos-tracingstore/conf/com.scalableminds.webknossos.tracingstore.routes
@@ -27,6 +27,7 @@ POST        /volume/mergedFromContents                          @com.scalablemin
 # Zarr endpoints for volume annotations
 GET         /volume/zarr/:tracingId                             @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.volumeTracingFolderContent(token: Option[String], tracingId: String)
 GET         /volume/zarr/:tracingId/.zgroup                     @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.zGroup(token: Option[String], tracingId: String)
+GET         /volume/zarr/:tracingId/.zattrs                     @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.zAttrs(token: Option[String], tracingId: String)
 GET         /volume/zarr/:tracingId/:mag                        @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.volumeTracingMagFolderContent(token: Option[String], tracingId: String, mag: String)
 GET         /volume/zarr/:tracingId/:mag/.zarray                @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.zArray(token: Option[String], tracingId: String, mag: String)
 GET         /volume/zarr/:tracingId/:mag/:cxyz                  @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.rawZarrCube(token: Option[String], tracingId: String, mag: String, cxyz: String)