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Use zarr string fill values #7017

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merged 8 commits into from
May 2, 2023
Merged

Use zarr string fill values #7017

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adc5ead
Use string fill values
frcroth Apr 25, 2023
329058c
Update Changelog
frcroth Apr 25, 2023
3796297
Merge branch 'master' into zarr-string-fill-values
frcroth Apr 25, 2023
1a2fbf3
Update webknossos-datastore/app/com/scalableminds/webknossos/datastor…
frcroth Apr 28, 2023
661b740
Merge branch 'master' into zarr-string-fill-values
frcroth Apr 28, 2023
5c92233
Merge branch 'master' into zarr-string-fill-values
frcroth May 2, 2023
fd1213d
Merge branch 'master' into zarr-string-fill-values
frcroth May 2, 2023
282db2b
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frcroth May 2, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.unreleased.md
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Expand Up @@ -18,6 +18,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released

### Fixed
- Fixed that changing a segment color could lead to a crash. [#7000](https://github.com/scalableminds/webknossos/pull/7000)
- The fill_value property of zarr dataset is now used when it is not a number. [#7017](https://github.com/scalableminds/webknossos/pull/7017)
- Fixed rendering issues on some affected systems that led to "black holes". [#7018](https://github.com/scalableminds/webknossos/pull/7018)
- Fixed a bug that made downloads of public annotations fail occasionally. [#7025](https://github.com/scalableminds/webknossos/pull/7025)
- Added a workaround for a WebGL crash which could appear when a dataset contained many segmentation layers. [#6995](https://github.com/scalableminds/webknossos/pull/6995)
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28 changes: 28 additions & 0 deletions ...ssos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/ArrayDataType.scala
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Expand Up @@ -19,4 +19,32 @@ object ArrayDataType extends ExtendedEnumeration {
case ArrayDataType.i1 => 1
case ArrayDataType.u1 => 1
}

def maxValue(dataType: ArrayDataType): Number =
dataType match {
case ArrayDataType.f8 => Double.MaxValue
case ArrayDataType.f4 => Float.MaxValue
case ArrayDataType.i8 => Long.MaxValue
case ArrayDataType.u8 => Long.MaxValue // Max value for primitive datatypes
case ArrayDataType.i4 => Int.MaxValue
case ArrayDataType.u4 => Math.pow(2, 4 * 8).toLong - 1
case ArrayDataType.i2 => Char.MaxValue
case ArrayDataType.u2 => Math.pow(2, 2 * 8).toLong - 1
case ArrayDataType.i1 => Byte.MaxValue
case ArrayDataType.u1 => Math.pow(2, 1 * 8).toLong - 1
}

def minValue(dataType: ArrayDataType): Number =
dataType match {
case ArrayDataType.f8 => Double.MinValue
case ArrayDataType.f4 => Float.MinValue
case ArrayDataType.i8 => Long.MinValue
case ArrayDataType.u8 => 0
case ArrayDataType.i4 => Int.MinValue
case ArrayDataType.u4 => 0
case ArrayDataType.i2 => Char.MinValue
case ArrayDataType.u2 => 0
case ArrayDataType.i1 => Byte.MinValue
case ArrayDataType.u1 => 0
}
}
10 changes: 9 additions & 1 deletion ...ssos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/DatasetHeader.scala
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Expand Up @@ -33,7 +33,7 @@ trait DatasetHeader {
lazy val fillValueNumber: Number =
fill_value match {
case Right(n) => n
case Left(_) => 0 // parsing fill value from string not currently supported
case Left(s) => parseFillValueFromString(s)
}

def boundingBox(axisOrder: AxisOrder): Option[BoundingBox] =
Expand All @@ -48,5 +48,13 @@ trait DatasetHeader {

def isSharded = false

private def parseFillValueFromString(s: String): Number =
s match {
case "NaN" => 0
case "Infinity" => ArrayDataType.maxValue(resolvedDataType)
case "-Infinity" => ArrayDataType.minValue(resolvedDataType)
case _ => 0 // Unsupported fill value does not throw exception
}

def voxelOffset: Array[Int]
}