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Merged
merged 4 commits into from
Oct 1, 2025
Merged

Make dataset compose voxel-size-aware #8962

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cd6a43d
Make dataset compose voxel-size-aware
fm3 Sep 30, 2025
9ba3843
remove voxel size from protocol, use inferred voxel size
fm3 Sep 30, 2025
640503f
In case of supplied transformations, do not shfit mags
fm3 Sep 30, 2025
c7a55f8
Merge branch 'master' into compose-voxel-size-aware
fm3 Oct 1, 2025
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21 changes: 14 additions & 7 deletions app/models/dataset/ComposeService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ package models.dataset
import com.scalableminds.util.accesscontext.DBAccessContext
import com.scalableminds.util.objectid.ObjectId
import com.scalableminds.util.tools.{Fox, FoxImplicits}
import com.scalableminds.webknossos.datastore.explore.ExploreLayerUtils
import com.scalableminds.webknossos.datastore.models.VoxelSize
import com.scalableminds.webknossos.datastore.models.datasource._
import models.user.User
Expand Down Expand Up @@ -36,7 +37,8 @@ object ComposeRequestLayer {

class ComposeService @Inject()(datasetDAO: DatasetDAO, dataStoreDAO: DataStoreDAO, datasetService: DatasetService)(
implicit ec: ExecutionContext)
extends FoxImplicits {
extends ExploreLayerUtils
with FoxImplicits {

def composeDataset(composeRequest: ComposeRequest, user: User)(
implicit ctx: DBAccessContext,
Expand All @@ -53,8 +55,9 @@ class ComposeService @Inject()(datasetDAO: DatasetDAO, dataStoreDAO: DataStoreDA

} yield (dataSource, dataset._id)

private def getLayerFromComposeLayer(composeLayer: ComposeRequestLayer)(implicit ctx: DBAccessContext,
mp: MessagesProvider): Fox[StaticLayer] =
private def getLayerFromComposeLayer(composeLayer: ComposeRequestLayer)(
implicit ctx: DBAccessContext,
mp: MessagesProvider): Fox[(StaticLayer, VoxelSize)] =
for {
dataset <- datasetDAO.findOne(composeLayer.datasetId) ?~> "Dataset not found"
usableDataSource <- datasetService.usableDataSourceFor(dataset)
Expand All @@ -71,7 +74,7 @@ class ComposeService @Inject()(datasetDAO: DatasetDAO, dataStoreDAO: DataStoreDA
coordinateTransformations = applyCoordinateTransformations(l.coordinateTransformations)))
case _ => Fox.failure("Unsupported layer type for composition: " + layer.getClass.getSimpleName)
}
} yield editedLayer
} yield (editedLayer, usableDataSource.scale)

private def isComposable(composeRequest: ComposeRequest)(implicit ctx: DBAccessContext): Fox[Boolean] =
// Check that all datasets are on the same data store
Expand All @@ -90,14 +93,18 @@ class ComposeService @Inject()(datasetDAO: DatasetDAO, dataStoreDAO: DataStoreDA
implicit ctx: DBAccessContext,
mp: MessagesProvider): Fox[UsableDataSource] =
for {
layers <- Fox.serialCombined(composeRequest.layers.toList)(getLayerFromComposeLayer(_))
layersAndVoxelSizes <- Fox.serialCombined(composeRequest.layers.toList)(getLayerFromComposeLayer)
(layers, voxelSize) <- if (composeRequest.layers.forall(_.transformations.isEmpty)) {
adaptLayersAndVoxelSize(layersAndVoxelSizes, None)
} else {
Fox.successful(layersAndVoxelSizes.map(_._1), composeRequest.voxelSize)
}
dataSource = UsableDataSource(
DataSourceId(datasetDirectoryName, organizationId),
layers,
composeRequest.voxelSize,
voxelSize,
None
)

} yield dataSource

}
2 changes: 1 addition & 1 deletion ...ssos-datastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLayerUtils.scala
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Expand Up @@ -18,7 +18,7 @@ import scala.util.Try

trait ExploreLayerUtils extends FoxImplicits {

def adaptLayersAndVoxelSize(
protected def adaptLayersAndVoxelSize(
layersWithVoxelSizes: List[(StaticLayer, VoxelSize)],
preferredVoxelSize: Option[VoxelSize])(implicit ec: ExecutionContext): Fox[(List[StaticLayer], VoxelSize)] =
for {
Expand Down