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98
...atastore/app/com/scalableminds/webknossos/datastore/explore/NeuroglancerUriExplorer.scala
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| package com.scalableminds.webknossos.datastore.explore | ||
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| import com.scalableminds.util.geometry.{Vec3Double, Vec3Int} | ||
| import com.scalableminds.util.tools.Fox | ||
| import com.scalableminds.webknossos.datastore.dataformats.n5.{N5DataLayer, N5SegmentationLayer} | ||
| import com.scalableminds.webknossos.datastore.dataformats.precomputed.{ | ||
| PrecomputedDataLayer, | ||
| PrecomputedSegmentationLayer | ||
| } | ||
| import com.scalableminds.webknossos.datastore.dataformats.zarr.{ZarrDataLayer, ZarrSegmentationLayer} | ||
| import com.scalableminds.webknossos.datastore.dataformats.zarr3.{Zarr3DataLayer, Zarr3SegmentationLayer} | ||
| import com.scalableminds.webknossos.datastore.datavault.VaultPath | ||
| import com.scalableminds.webknossos.datastore.models.datasource.LayerViewConfiguration.LayerViewConfiguration | ||
| import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, LayerViewConfiguration} | ||
| import com.scalableminds.webknossos.datastore.storage.{DataVaultService, RemoteSourceDescriptor} | ||
| import play.api.libs.json._ | ||
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| import java.net.URI | ||
| import javax.inject.Inject | ||
| import scala.concurrent.ExecutionContext | ||
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| class NeuroglancerUriExplorer @Inject()(dataVaultService: DataVaultService, | ||
| exploreLayerService: ExploreLayerService, | ||
| implicit val ec: ExecutionContext) | ||
| extends RemoteLayerExplorer { | ||
| override def name: String = "Neuroglancer URI Explorer" | ||
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| override def explore(remotePath: VaultPath, credentialId: Option[String]): Fox[List[(DataLayer, Vec3Double)]] = | ||
| for { | ||
| _ <- Fox.successful(()) | ||
| spec <- Json | ||
| .parse(remotePath.toUri.getFragment.drop(1)) | ||
| .validate[JsObject] | ||
| .toFox ?~> "Did not find JSON object in URI" | ||
| layerSpecs <- (spec \ "layers").validate[JsArray].toFox | ||
| _ <- Fox.bool2Fox(credentialId.isEmpty) ~> "Neuroglancer URI Explorer does not support credentials" | ||
| exploredLayers = layerSpecs.value.map(exploreNeuroglancerLayer).toList | ||
| layerLists <- Fox.combined(exploredLayers) | ||
| layers = layerLists.flatten | ||
| renamedLayers = exploreLayerService.makeLayerNamesUnique(layers.map(_._1)) | ||
| } yield renamedLayers.zip(layers.map(_._2)) | ||
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| private def exploreNeuroglancerLayer(layerSpec: JsValue): Fox[List[(DataLayer, Vec3Double)]] = | ||
| for { | ||
| _ <- Fox.successful(()) | ||
| obj <- layerSpec.validate[JsObject].toFox | ||
| source <- (obj \ "source").validate[JsString].toFox | ||
| layerType = new URI(source.value).getScheme | ||
| sourceURI = new URI(source.value.substring(f"$layerType://".length)) | ||
| name <- (obj \ "name").validate[JsString].toFox | ||
| remoteSourceDescriptor = RemoteSourceDescriptor(sourceURI, None) | ||
| remotePath <- dataVaultService.getVaultPath(remoteSourceDescriptor) ?~> "dataVault.setup.failed" | ||
| viewConfiguration = getViewConfig(obj) | ||
| layer <- exploreLayer(layerType, remotePath, name.value) | ||
| layerWithViewConfiguration <- assignViewConfiguration(layer, viewConfiguration) | ||
| } yield layerWithViewConfiguration | ||
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| private def exploreLayer(layerType: String, remotePath: VaultPath, name: String): Fox[List[(DataLayer, Vec3Double)]] = | ||
| layerType match { | ||
| case "n5" => | ||
| Fox.firstSuccess( | ||
| Seq(new N5ArrayExplorer().explore(remotePath, None), new N5MultiscalesExplorer().explore(remotePath, None))) | ||
| case "precomputed" => new PrecomputedExplorer().explore(remotePath, None) | ||
| case "zarr" | "zarr2" => | ||
| Fox.firstSuccess( | ||
| Seq(new NgffExplorer().explore(remotePath, None), | ||
| new ZarrArrayExplorer(Vec3Int.ones, ec).explore(remotePath, None))) | ||
| case "zarr3" => new Zarr3ArrayExplorer().explore(remotePath, None) | ||
| case _ => Fox.failure(f"Can not explore layer of $layerType type") | ||
| } | ||
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| private def getViewConfig(layerSpec: JsObject): LayerViewConfiguration = { | ||
| val opacity = (layerSpec \ "opacity").validate[Double].getOrElse(1.0) | ||
| val intensityRange = (layerSpec \ "shaderControls" \ "normalized" \ "range").validate[JsArray].asOpt | ||
| val options = Seq("alpha" -> JsNumber(opacity * 100)) ++ intensityRange.map("intensityRange" -> _) | ||
| options.toMap | ||
| } | ||
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| private def assignViewConfiguration( | ||
| value: List[(DataLayer, Vec3Double)], | ||
| configuration: LayerViewConfiguration.LayerViewConfiguration): Fox[List[(DataLayer, Vec3Double)]] = | ||
| for { | ||
| _ <- Fox.successful(()) | ||
| layers = value.map(_._1) | ||
| layersWithViewConfigs = layers.map { | ||
| case l: ZarrDataLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: ZarrSegmentationLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: N5DataLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: N5SegmentationLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: PrecomputedDataLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: PrecomputedSegmentationLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: Zarr3DataLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
| case l: Zarr3SegmentationLayer => l.copy(defaultViewConfiguration = Some(configuration)) | ||
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| } | ||
| } yield layersWithViewConfigs.zip(value.map(_._2)) | ||
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| } |