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Add uint24 support for DatasetArray-based formats (excepting ND) #7413

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merged 4 commits into from
Nov 1, 2023
Merged

Add uint24 support for DatasetArray-based formats (excepting ND) #7413

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bf90b1a
Add uint24 support for DatasetArray-based formats (excepting ND)
fm3 Oct 26, 2023
1603f66
changelog
fm3 Oct 26, 2023
ca21a08
Merge branch 'master' into zarr3-uint24
fm3 Oct 26, 2023
1f0e082
Merge branch 'master' into zarr3-uint24
fm3 Nov 1, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.unreleased.md
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Expand Up @@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
[Commits](https://github.com/scalableminds/webknossos/compare/23.11.0...HEAD)

### Added
- Added support for reading uint24 rgb layers in datasets with zarr2/zarr3/n5/neuroglancerPrecomputed format, as used for voxelytics predictions. [#7413](https://github.com/scalableminds/webknossos/pull/7413)

### Changed

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5 changes: 2 additions & 3 deletions ...atastore/app/com/scalableminds/webknossos/datastore/dataformats/n5/N5BucketProvider.scala
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Expand Up @@ -7,8 +7,7 @@ import com.scalableminds.webknossos.datastore.dataformats.{BucketProvider, DataC
import com.scalableminds.webknossos.datastore.datareaders.n5.N5Array
import com.scalableminds.webknossos.datastore.datavault.VaultPath
import com.scalableminds.webknossos.datastore.models.BucketPosition
import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId
import com.scalableminds.webknossos.datastore.models.datasource.DataLayer
import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
import com.scalableminds.webknossos.datastore.models.requests.DataReadInstruction
import com.scalableminds.webknossos.datastore.storage.RemoteSourceDescriptorService
import com.typesafe.scalalogging.LazyLogging
Expand All @@ -22,7 +21,7 @@ class N5CubeHandle(n5Array: N5Array) extends DataCubeHandle with LazyLogging {
def cutOutBucket(bucket: BucketPosition, dataLayer: DataLayer)(implicit ec: ExecutionContext): Fox[Array[Byte]] = {
val shape = Vec3Int.full(bucket.bucketLength)
val offset = Vec3Int(bucket.topLeft.voxelXInMag, bucket.topLeft.voxelYInMag, bucket.topLeft.voxelZInMag)
n5Array.readBytesXYZ(shape, offset)
n5Array.readBytesXYZ(shape, offset, dataLayer.elementClass == ElementClass.uint24)
}

override protected def onFinalize(): Unit = ()
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5 changes: 2 additions & 3 deletions ...calableminds/webknossos/datastore/dataformats/precomputed/PrecomputedBucketProvider.scala
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Expand Up @@ -7,8 +7,7 @@ import com.scalableminds.webknossos.datastore.dataformats.{BucketProvider, DataC
import com.scalableminds.webknossos.datastore.datareaders.precomputed.PrecomputedArray
import com.scalableminds.webknossos.datastore.datavault.VaultPath
import com.scalableminds.webknossos.datastore.models.BucketPosition
import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId
import com.scalableminds.webknossos.datastore.models.datasource.DataLayer
import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
import com.scalableminds.webknossos.datastore.models.requests.DataReadInstruction
import com.scalableminds.webknossos.datastore.storage.RemoteSourceDescriptorService
import com.typesafe.scalalogging.LazyLogging
Expand All @@ -22,7 +21,7 @@ class PrecomputedCubeHandle(precomputedArray: PrecomputedArray) extends DataCube
def cutOutBucket(bucket: BucketPosition, dataLayer: DataLayer)(implicit ec: ExecutionContext): Fox[Array[Byte]] = {
val shape = Vec3Int.full(bucket.bucketLength)
val offset = Vec3Int(bucket.topLeft.voxelXInMag, bucket.topLeft.voxelYInMag, bucket.topLeft.voxelZInMag)
precomputedArray.readBytesXYZ(shape, offset)
precomputedArray.readBytesXYZ(shape, offset, dataLayer.elementClass == ElementClass.uint24)
}

override protected def onFinalize(): Unit = ()
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5 changes: 2 additions & 3 deletions ...tore/app/com/scalableminds/webknossos/datastore/dataformats/zarr/ZarrBucketProvider.scala
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Expand Up @@ -7,8 +7,7 @@ import com.scalableminds.webknossos.datastore.dataformats.{BucketProvider, DataC
import com.scalableminds.webknossos.datastore.datareaders.zarr.ZarrArray
import com.scalableminds.webknossos.datastore.datavault.VaultPath
import com.scalableminds.webknossos.datastore.models.BucketPosition
import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId
import com.scalableminds.webknossos.datastore.models.datasource.DataLayer
import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
import com.scalableminds.webknossos.datastore.models.requests.DataReadInstruction
import com.scalableminds.webknossos.datastore.storage.RemoteSourceDescriptorService
import com.typesafe.scalalogging.LazyLogging
Expand All @@ -26,7 +25,7 @@ class ZarrCubeHandle(zarrArray: ZarrArray) extends DataCubeHandle with LazyLoggi
bucket.additionalCoordinates match {
case Some(additionalCoordinates) if additionalCoordinates.nonEmpty =>
zarrArray.readBytesWithAdditionalCoordinates(shape, offset, additionalCoordinates, dataLayer.additionalAxisMap)
case _ => zarrArray.readBytesXYZ(shape, offset)
case _ => zarrArray.readBytesXYZ(shape, offset, dataLayer.elementClass == ElementClass.uint24)
}
}

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5 changes: 2 additions & 3 deletions ...re/app/com/scalableminds/webknossos/datastore/dataformats/zarr3/Zarr3BucketProvider.scala
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Expand Up @@ -7,8 +7,7 @@ import com.scalableminds.webknossos.datastore.dataformats.{BucketProvider, DataC
import com.scalableminds.webknossos.datastore.datareaders.zarr3.Zarr3Array
import com.scalableminds.webknossos.datastore.datavault.VaultPath
import com.scalableminds.webknossos.datastore.models.BucketPosition
import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId
import com.scalableminds.webknossos.datastore.models.datasource.DataLayer
import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
import com.scalableminds.webknossos.datastore.models.requests.DataReadInstruction
import com.scalableminds.webknossos.datastore.storage.RemoteSourceDescriptorService
import com.typesafe.scalalogging.LazyLogging
Expand All @@ -22,7 +21,7 @@ class ZarrCubeHandle(zarrArray: Zarr3Array) extends DataCubeHandle with LazyLogg
def cutOutBucket(bucket: BucketPosition, dataLayer: DataLayer)(implicit ec: ExecutionContext): Fox[Array[Byte]] = {
val shape = Vec3Int.full(bucket.bucketLength)
val offset = Vec3Int(bucket.topLeft.voxelXInMag, bucket.topLeft.voxelYInMag, bucket.topLeft.voxelZInMag)
zarrArray.readBytesXYZ(shape, offset)
zarrArray.readBytesXYZ(shape, offset, dataLayer.elementClass == ElementClass.uint24)
}

override protected def onFinalize(): Unit = ()
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9 changes: 7 additions & 2 deletions ...ossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/DatasetArray.scala
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Expand Up @@ -56,14 +56,19 @@ class DatasetArray(vaultPath: VaultPath,
}

// Returns byte array in fortran-order with little-endian values
def readBytesXYZ(shape: Vec3Int, offset: Vec3Int)(implicit ec: ExecutionContext): Fox[Array[Byte]] = {
def readBytesXYZ(shape: Vec3Int, offset: Vec3Int, shouldReadUint24: Boolean = false)(
implicit ec: ExecutionContext): Fox[Array[Byte]] = {
val paddingDimensionsCount = rank - 3
val offsetArray = channelIndex match {
case Some(c) if rank >= 4 =>
Array.fill(paddingDimensionsCount - 1)(0) :+ c :+ offset.x :+ offset.y :+ offset.z
case _ => Array.fill(paddingDimensionsCount)(0) :+ offset.x :+ offset.y :+ offset.z
}
val shapeArray = Array.fill(paddingDimensionsCount)(1) :+ shape.x :+ shape.y :+ shape.z
val shapeArray = if (shouldReadUint24 && rank >= 4) {
Array.fill(paddingDimensionsCount - 1)(1) :+ 3 :+ shape.x :+ shape.y :+ shape.z
} else {
Array.fill(paddingDimensionsCount)(1) :+ shape.x :+ shape.y :+ shape.z
}

readBytes(shapeArray, offsetArray)
}
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