Automatically assign color and channel name for omero ngff

CHANGELOG.unreleased.md

@@ -20,7 +20,8 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - OpenID Connect authorization can now use a client secret for added security. [#7263](https://github.com/scalableminds/webknossos/pull/7263)
 
 ### Changed
-- Small messages during annotating (e.g. “finished undo”, “applying mapping…”) are now click-through so they do not block users from selecting tools. [7239](https://github.com/scalableminds/webknossos/pull/7239)
+- Small messages during annotating (e.g. “finished undo”, “applying mapping…”) are now click-through, so they do not block users from selecting tools. [#7239](https://github.com/scalableminds/webknossos/pull/7239)
+- When exploring remote NGFF datasets with channels, layer names and colors are automatically imported if available in the metadata. [#7251](https://github.com/scalableminds/webknossos/pull/7251)
 - Annotating volume data uses a transaction-based mechanism now. As a result, WK is more robust against partial saves (i.e., due to a crashing tab). [#7264](https://github.com/scalableminds/webknossos/pull/7264)
 - Improved speed of saving volume data. [#7264](https://github.com/scalableminds/webknossos/pull/7264)
 - Improved progress indicator when saving volume data. [#7264](https://github.com/scalableminds/webknossos/pull/7264)

MIGRATIONS.unreleased.md

@@ -16,7 +16,7 @@ UPDATE webknossos.multiUsers SET isEmailVerified = false;
 
 - When interacting with webknossos via the python library, make sure you update to the latest version, as the task and project api have changed. Compare [webknossos-libs#930](https://github.com/scalableminds/webknossos-libs/pull/930). [#7220](https://github.com/scalableminds/webknossos/pull/7220)
 
- - If you have OIDC authentication set up, you can now remove the config keys `singleSignOn.openIdConnect.publicKey` and `singleSignOn.openIdConnect.publicKeyAlgorithm`, as the server’s public key is now automatically fetched. [7267](https://github.com/scalableminds/webknossos/pull/7267)
+ - If you have OIDC authentication set up, you can now remove the config keys `singleSignOn.openIdConnect.publicKey` and `singleSignOn.openIdConnect.publicKeyAlgorithm`, as the server’s public key is now automatically fetched. [#7267](https://github.com/scalableminds/webknossos/pull/7267)
 
 ### Postgres Evolutions:
 - [105-verify-email.sql](conf/evolutions/105-verify-email.sql)

app/models/binary/explore/NgffExplorer.scala

@@ -1,13 +1,16 @@
 package models.binary.explore
 
 import com.scalableminds.util.geometry.{Vec3Double, Vec3Int}
-import com.scalableminds.util.tools.Fox
+import com.scalableminds.util.image.Color
+import com.scalableminds.util.tools.{Fox, TextUtils}
 import com.scalableminds.webknossos.datastore.dataformats.MagLocator
 import com.scalableminds.webknossos.datastore.dataformats.zarr.{ZarrDataLayer, ZarrLayer, ZarrSegmentationLayer}
 import com.scalableminds.webknossos.datastore.datareaders.AxisOrder
 import com.scalableminds.webknossos.datastore.datareaders.zarr._
 import com.scalableminds.webknossos.datastore.datavault.VaultPath
-import com.scalableminds.webknossos.datastore.models.datasource.{Category, ElementClass}
+import com.scalableminds.webknossos.datastore.models.datasource.LayerViewConfiguration.LayerViewConfiguration
+import com.scalableminds.webknossos.datastore.models.datasource.{Category, ElementClass, LayerViewConfiguration}
+import play.api.libs.json.{JsArray, JsNumber}
 
 import scala.concurrent.ExecutionContext
 
@@ -25,7 +28,8 @@ class NgffExplorer(implicit val ec: ExecutionContext) extends RemoteLayerExplore
       layerLists: List[List[(ZarrLayer, Vec3Double)]] <- Fox.serialCombined(ngffHeader.multiscales)(multiscale => {
         for {
           channelCount: Int <- getNgffMultiscaleChannelCount(multiscale, remotePath)
-          layers <- layersFromNgffMultiscale(multiscale, remotePath, credentialId, channelCount)
+          channelAttributes = getChannelAttributes(ngffHeader)
+          layers <- layersFromNgffMultiscale(multiscale, remotePath, credentialId, channelCount, channelAttributes)
         } yield layers
       })
       layers: List[(ZarrLayer, Vec3Double)] = layerLists.flatten
@@ -48,6 +52,7 @@ class NgffExplorer(implicit val ec: ExecutionContext) extends RemoteLayerExplore
                                        remotePath: VaultPath,
                                        credentialId: Option[String],
                                        channelCount: Int,
+                                       channelAttributes: Option[Seq[ChannelAttributes]] = None,
                                        isSegmentation: Boolean = false): Fox[List[(ZarrLayer, Vec3Double)]] =
     for {
       axisOrder <- extractAxisOrder(multiscale.axes) ?~> "Could not extract XYZ axis order mapping. Does the data have x, y and z axes, stated in multiscales metadata?"
@@ -66,18 +71,55 @@ class NgffExplorer(implicit val ec: ExecutionContext) extends RemoteLayerExplore
           elementClassRaw <- elementClassFromMags(magsWithAttributes) ?~> "Could not extract element class from mags"
           elementClass = if (isSegmentation) ensureElementClassForSegmentationLayer(elementClassRaw)
           else elementClassRaw
+
+          (viewConfig: LayerViewConfiguration, channelName: String) = channelAttributes match {
+            case Some(attributes) => {
+              val color = attributes(channelIndex).color
+              val attributeName: String =
+                attributes(channelIndex).name
+                  .map(TextUtils.normalizeStrong(_).getOrElse(name).replaceAll(" ", ""))
+                  .getOrElse(name)
+              (color match {
+                case Some(c) => Seq(("color" -> JsArray(c.toArrayOfInts.map(i => JsNumber(BigDecimal(i)))))).toMap
+                case None    => LayerViewConfiguration.empty
+              }, attributeName)
+            }
+            case None => (LayerViewConfiguration.empty, name)
+          }
+
           boundingBox = boundingBoxFromMags(magsWithAttributes)
           layer: ZarrLayer = if (looksLikeSegmentationLayer(name, elementClass) || isSegmentation) {
-            ZarrSegmentationLayer(name,
+            ZarrSegmentationLayer(channelName,
                                   boundingBox,
                                   elementClass,
                                   magsWithAttributes.map(_.mag),
-                                  largestSegmentId = None)
-          } else ZarrDataLayer(name, Category.color, boundingBox, elementClass, magsWithAttributes.map(_.mag))
+                                  largestSegmentId = None,
+                                  defaultViewConfiguration = Some(viewConfig))
+          } else
+            ZarrDataLayer(channelName,
+                          Category.color,
+                          boundingBox,
+                          elementClass,
+                          magsWithAttributes.map(_.mag),
+                          defaultViewConfiguration = Some(viewConfig))
         } yield (layer, voxelSizeNanometers)
       })
     } yield layerTuples
 
+  private case class ChannelAttributes(color: Option[Color], name: Option[String])
+
+  private def getChannelAttributes(
+      ngffHeader: NgffMetadata
+  ): Option[Seq[ChannelAttributes]] =
+    ngffHeader.omero match {
+      case Some(value) =>
+        Some(
+          value.channels.map(omeroChannelAttributes =>
+            ChannelAttributes(omeroChannelAttributes.color.map(Color.fromHTML(_).getOrElse(Color(1, 1, 1, 0))),
+                              omeroChannelAttributes.label)))
+      case None => None
+    }
+
   private def exploreLabelLayers(remotePath: VaultPath,
                                  credentialId: Option[String]): Fox[List[(ZarrLayer, Vec3Double)]] =
     for {

util/src/main/scala/com/scalableminds/util/image/Color.scala

@@ -1,11 +1,13 @@
 package com.scalableminds.util.image
 
 import com.scalableminds.util.tools.ExtendedTypes._
+import net.liftweb.common.Box.tryo
 import play.api.libs.json.Json._
 import play.api.libs.json.{Format, JsValue, _}
 
 case class Color(r: Double, g: Double, b: Double, a: Double) {
-  def toHtml = "#%02x%02x%02x".format((r * 255).toInt, (g * 255).toInt, (b * 255).toInt)
+  def toHtml: String = "#%02x%02x%02x".format((r * 255).toInt, (g * 255).toInt, (b * 255).toInt)
+  def toArrayOfInts: Array[Int] = Array((r * 255).toInt, (g * 255).toInt, (b * 255).toInt)
 }
 
 object Color {
@@ -21,6 +23,15 @@ object Color {
     )
   }
 
+  def fromHTML(htmlCode: String): Option[Color] =
+    tryo({
+      val code = if (!htmlCode.startsWith("#")) s"#$htmlCode" else htmlCode
+      val r = Integer.valueOf(code.substring(1, 3), 16) / 255d
+      val g = Integer.valueOf(code.substring(3, 5), 16) / 255d
+      val b = Integer.valueOf(code.substring(5, 7), 16) / 255d
+      Color(r, g, b, 0)
+    }).toOption
+
   implicit object ColorFormat extends Format[Color] {
 
     def writes(c: Color) = if (c.a == 1) Json.arr(c.r, c.g, c.b) else Json.arr(c.r, c.g, c.b, c.a)

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

@@ -84,7 +84,7 @@ object NgffMultiscalesItem {
   implicit val jsonFormat: OFormat[NgffMultiscalesItem] = Json.format[NgffMultiscalesItem]
 }
 
-case class NgffMetadata(multiscales: List[NgffMultiscalesItem])
+case class NgffMetadata(multiscales: List[NgffMultiscalesItem], omero: Option[NgffOmeroMetadata])
 
 object NgffMetadata {
   def fromNameScaleAndMags(dataLayerName: String, dataSourceScale: Vec3Double, mags: List[Vec3Int]): NgffMetadata = {
@@ -93,7 +93,7 @@ object NgffMetadata {
         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)))
+    NgffMetadata(multiscales = List(NgffMultiscalesItem(name = Some(dataLayerName), datasets = datasets)), None)
   }
 
   implicit val jsonFormat: OFormat[NgffMetadata] = Json.format[NgffMetadata]
@@ -107,3 +107,13 @@ object NgffLabelsGroup {
   implicit val jsonFormat: OFormat[NgffLabelsGroup] = Json.format[NgffLabelsGroup]
   val LABEL_PATH = "labels/.zattrs"
 }
+
+case class NgffOmeroMetadata(channels: List[NgffChannelAttributes])
+object NgffOmeroMetadata {
+  implicit val jsonFormat: OFormat[NgffOmeroMetadata] = Json.format[NgffOmeroMetadata]
+}
+
+case class NgffChannelAttributes(color: Option[String], label: Option[String])
+object NgffChannelAttributes {
+  implicit val jsonFormat: OFormat[NgffChannelAttributes] = Json.format[NgffChannelAttributes]
+}

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataLayer.scala

@@ -143,6 +143,8 @@ object ElementClass extends ExtendedEnumeration {
 object LayerViewConfiguration {
   type LayerViewConfiguration = Map[String, JsValue]
 
+  def empty: LayerViewConfiguration = Map()
+
   implicit val jsonFormat: Format[LayerViewConfiguration] = Format.of[LayerViewConfiguration]
 }