Support OME-NGFF zarr dataset translation

CHANGELOG.unreleased.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added the option for "Selective Segment Visibility" for segmentation layers. Select this option in the left sidebar to only show segments that are currently active or hovered.  [#8281](https://github.com/scalableminds/webknossos/pull/8281)
 - A segment can be activated with doubleclick now. [#8281](https://github.com/scalableminds/webknossos/pull/8281)
 - It is now possible to select the magnification of the layers on which an AI model will be trained. [#8266](https://github.com/scalableminds/webknossos/pull/8266)
+- Added support for translations in OME NGFF zarr datasets (translation within coordinateTransformations on datasets). [#8311](https://github.com/scalableminds/webknossos/pull/8311)
 
 ### Changed
 - Renamed "resolution" to "magnification" in more places within the codebase, including local variables. [#8168](https://github.com/scalableminds/webknossos/pull/8168)

webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadata.scala

@@ -36,8 +36,11 @@ object NgffMetadata {
       mag =>
         NgffDataset(
           path = mag.toMagLiteral(allowScalar = true),
-          List(NgffCoordinateTransformation(
-            scale = Some(List[Double](1.0) ++ (dataSourceVoxelSize.factor * Vec3Double(mag)).toList)))
+          List(
+            NgffCoordinateTransformation(
+              scale = Some(List[Double](1.0) ++ (dataSourceVoxelSize.factor * Vec3Double(mag)).toList),
+              translation = Some(List[Double](0.0, 0.0, 0.0))
+            ))
       ))
     val lengthUnitStr = dataSourceVoxelSize.unit.toString
     val axes = List(

webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadataV0_5.scala

@@ -44,8 +44,10 @@ object NgffMetadataV0_5 {
       mag =>
         NgffDataset(
           path = mag.toMagLiteral(allowScalar = true),
-          List(NgffCoordinateTransformation(
-            scale = Some(List[Double](1.0) ++ (dataSourceVoxelSize.factor * Vec3Double(mag)).toList)))
+          List(
+            NgffCoordinateTransformation(
+              scale = Some(List[Double](1.0) ++ (dataSourceVoxelSize.factor * Vec3Double(mag)).toList),
+              translation = Some(List[Double](0.0, 0.0, 0.0))))
       ))
     val lengthUnitStr = dataSourceVoxelSize.unit.toString
     val axes = List(NgffAxis(name = "c", `type` = "channel")) ++ additionalAxes

webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/SharedNgffMetadataAttributes.scala

@@ -5,7 +5,9 @@ import com.scalableminds.webknossos.datastore.models.{LengthUnit, VoxelSize}
 import net.liftweb.common.{Box, Failure, Full}
 import play.api.libs.json.{Json, OFormat}
 
-case class NgffCoordinateTransformation(`type`: String = "scale", scale: Option[List[Double]])
+case class NgffCoordinateTransformation(`type`: String = "scale",
+                                        scale: Option[List[Double]],
+                                        translation: Option[List[Double]])
 
 object NgffCoordinateTransformation {
   implicit val jsonFormat: OFormat[NgffCoordinateTransformation] = Json.format[NgffCoordinateTransformation]
@@ -17,17 +19,19 @@ object NgffDataset {
   implicit val jsonFormat: OFormat[NgffDataset] = Json.format[NgffDataset]
 }
 
-case class NgffAxis(name: String, `type`: String, unit: Option[String] = None) {
+case class NgffAxis(name: String, `type`: String, unit: Option[String] = None, units: Option[String] = None) {
 
-  def lengthUnit: Box[models.LengthUnit.Value] =
+  def lengthUnit: Box[models.LengthUnit.Value] = {
+    val u = units.orElse(unit)
     if (`type` != "space")
       Failure(f"Could not convert NGFF unit $name of type ${`type`} to LengthUnit")
     else {
-      unit match {
+      u match {
         case None | Some("") => Full(VoxelSize.DEFAULT_UNIT)
         case Some(someUnit)  => LengthUnit.fromString(someUnit)
       }
     }
+  }
 }
 
 object NgffAxis {

webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLayerUtils.scala

@@ -50,8 +50,8 @@ trait ExploreLayerUtils extends FoxImplicits {
                                                    preferredVoxelSize: Option[VoxelSize],
                                                    voxelSize: VoxelSize): List[DataLayerWithMagLocators] =
     layers.map(l => {
-      val coordinateTransformations = coordinateTransformationForVoxelSize(voxelSize, preferredVoxelSize)
-      l.mapped(coordinateTransformations = coordinateTransformations)
+      val generatedCoordinateTransformation = coordinateTransformationForVoxelSize(voxelSize, preferredVoxelSize)
+      l.mapped(coordinateTransformations = generatedCoordinateTransformation.orElse(l.coordinateTransformations))
     })
 
   private def isPowerOfTwo(x: Int): Boolean =

webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorationUtils.scala

@@ -5,26 +5,12 @@ import com.scalableminds.util.image.Color
 import com.scalableminds.util.tools.TextUtils.normalizeStrong
 import com.scalableminds.util.tools.{Fox, FoxImplicits, TextUtils}
 import com.scalableminds.webknossos.datastore.datareaders.AxisOrder
-import com.scalableminds.webknossos.datastore.datareaders.zarr.{
-  NgffAxis,
-  NgffChannelWindow,
-  NgffCoordinateTransformation,
-  NgffDataset,
-  NgffLabelsGroup,
-  NgffMultiscalesItem,
-  NgffMultiscalesItemV0_5,
-  NgffOmeroMetadata
-}
+import com.scalableminds.webknossos.datastore.datareaders.zarr.{NgffAxis, NgffChannelWindow, NgffCoordinateTransformation, NgffDataset, NgffLabelsGroup, NgffMultiscalesItem, NgffMultiscalesItemV0_5, NgffOmeroMetadata}
 import com.scalableminds.webknossos.datastore.datavault.VaultPath
 import com.scalableminds.webknossos.datastore.models.{LengthUnit, VoxelSize}
 import com.scalableminds.webknossos.datastore.models.LengthUnit.LengthUnit
 import com.scalableminds.webknossos.datastore.models.datasource.LayerViewConfiguration.LayerViewConfiguration
-import com.scalableminds.webknossos.datastore.models.datasource.{
-  AdditionalAxis,
-  DataLayerWithMagLocators,
-  ElementClass,
-  LayerViewConfiguration
-}
+import com.scalableminds.webknossos.datastore.models.datasource.{AdditionalAxis, CoordinateTransformation, CoordinateTransformationType, DataLayerWithMagLocators, ElementClass, LayerViewConfiguration}
 import net.liftweb.common.Box
 import play.api.libs.json.{JsArray, JsBoolean, JsNumber, Json}
 
@@ -259,6 +245,42 @@ trait NgffExplorationUtils extends FoxImplicits {
       layerAndVoxelSizeTuples = layers.map((_, VoxelSize(voxelSizeFactor, unifiedAxisUnit)))
     } yield layerAndVoxelSizeTuples
 
+  protected def getTranslation(multiscale: NgffMultiscalesItem): Option[List[CoordinateTransformation]] = {
+    val is2d = !multiscale.axes.exists(_.name == "z")
+    val baseTranslation = if (is2d) List(1.0, 1.0) else List(1.0, 1.0, 1.0)
+    if (!multiscale.datasets.head.coordinateTransformations.exists(_.`type` == "translation")) {
+      None
+    } else {
+      var translation = multiscale.datasets.head.coordinateTransformations.foldLeft(baseTranslation)((acc, ct) => {
+        ct.`type` match {
+          case "translation" =>
+            ct.translation match {
+              case Some(translationList) =>
+                acc.zipWithIndex.map { case (v, i) => v * translationList(translationList.length - 1 - i) }
+              case _ => acc
+            }
+          case _ =>
+            ct.scale match {
+              case Some(scaleList) => acc.zipWithIndex.map { case (v, i) => v / scaleList(scaleList.length - 1 - i) }
+              case _ => acc
+            }
+        }
+      })
+      if (is2d) {
+        translation = translation :+ 0.0
+      }
+      val xTranslation = translation(0)
+      val yTranslation = translation(1)
+      val zTranslation = translation(2)
+      val coordinateTransformation = CoordinateTransformation(
+        `type` = CoordinateTransformationType.affine,
+        matrix = Some(
+          List(List(1, 0, 0, xTranslation), List(0, 1, 0, yTranslation), List(0, 0, 1, zTranslation), List(0, 0, 0, 1)))
+      )
+      Some(List(coordinateTransformation))
+    }
+  }
+
   protected def layersForLabel(remotePath: VaultPath,
                                labelPath: String,
                                credentialId: Option[String]): Fox[List[(DataLayerWithMagLocators, VoxelSize)]]

webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffV0_4Explorer.scala

@@ -22,8 +22,8 @@ class NgffV0_4Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
     for {
       zattrsPath <- Fox.successful(remotePath / NgffMetadata.FILENAME_DOT_ZATTRS)
       ngffHeader <- zattrsPath.parseAsJson[NgffMetadata] ?~> s"Failed to read OME NGFF header at $zattrsPath"
-      labelLayers <- exploreLabelLayers(remotePath, credentialId).orElse(
-        Fox.successful(List[(DataLayerWithMagLocators, VoxelSize)]()))
+      //labelLayers <- exploreLabelLayers(remotePath, credentialId).orElse(
+      // Fox.successful(List[(DataLayerWithMagLocators, VoxelSize)]()))
 
       layerLists: List[List[(DataLayerWithMagLocators, VoxelSize)]] <- Fox.serialCombined(ngffHeader.multiscales)(
         multiscale => {
@@ -34,7 +34,7 @@ class NgffV0_4Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
           } yield layers
         })
       layers: List[(DataLayerWithMagLocators, VoxelSize)] = layerLists.flatten
-    } yield layers ++ labelLayers
+    } yield layers //++ labelLayers
 
   protected def createLayer(remotePath: VaultPath,
                             credentialId: Option[String],
@@ -58,6 +58,7 @@ class NgffV0_4Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
                                                                                          channelIndex)
       boundingBox = boundingBoxFromMags(magsWithAttributes)
       additionalAxes <- getAdditionalAxes(multiscale, remotePath)
+      translationOpt = getTranslation(multiscale)
       layer: ZarrLayer = if (looksLikeSegmentationLayer(datasetName, elementClass) || isSegmentation) {
         ZarrSegmentationLayer(
           channelName,
@@ -67,6 +68,7 @@ class NgffV0_4Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
           largestSegmentId = None,
           additionalAxes = Some(additionalAxes),
           defaultViewConfiguration = Some(viewConfig),
+          coordinateTransformations = translationOpt,
           dataFormat = DataFormat.zarr
         )
       } else
@@ -78,6 +80,7 @@ class NgffV0_4Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
           magsWithAttributes.map(_.mag),
           additionalAxes = Some(additionalAxes),
           defaultViewConfiguration = Some(viewConfig),
+          coordinateTransformations = translationOpt,
           dataFormat = DataFormat.zarr
         )
     } yield layer

webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffV0_5Explorer.scala

@@ -61,6 +61,7 @@ class NgffV0_5Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
 
       boundingBox = boundingBoxFromMags(magsWithAttributes)
       additionalAxes <- getAdditionalAxes(multiscale, remotePath)
+      translationOpt = getTranslation(multiscale)
       layer: Zarr3Layer = if (looksLikeSegmentationLayer(datasetName, elementClass) || isSegmentation) {
         Zarr3SegmentationLayer(
           channelName,
@@ -70,6 +71,7 @@ class NgffV0_5Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
           largestSegmentId = None,
           additionalAxes = Some(additionalAxes),
           defaultViewConfiguration = Some(viewConfig),
+          coordinateTransformations = translationOpt,
         )
       } else
         Zarr3DataLayer(
@@ -80,6 +82,7 @@ class NgffV0_5Explorer(implicit val ec: ExecutionContext) extends RemoteLayerExp
           magsWithAttributes.map(_.mag),
           additionalAxes = Some(additionalAxes),
           defaultViewConfiguration = Some(viewConfig),
+          coordinateTransformations = translationOpt,
         )
     } yield layer