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support reading zstd-compressed zarr2 datasets #7964

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merged 3 commits into from
Aug 5, 2024
Merged

support reading zstd-compressed zarr2 datasets #7964

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2f3454d
support reading zstd-compressed zarr2 datasets
fm3 Jul 31, 2024
8ef41fa
changelog
fm3 Jul 31, 2024
ec49b2a
Merge branch 'master' into zarr2-zstd
fm3 Aug 5, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.unreleased.md
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
- The context menu entry "Focus in Segment List" expands all necessary segment groups in the segments tab to show the highlighted segment. [#7950](https://github.com/scalableminds/webknossos/pull/7950)
- In the proofreading mode, you can enable/disable that only the active segment and the hovered segment are rendered. [#7654](https://github.com/scalableminds/webknossos/pull/7654)
- Upgraded s3 client for improved performance when loading remote datasets. [#7936](https://github.com/scalableminds/webknossos/pull/7936)
- Added support for reading zstd-compressed zarr2 datasets [#7964](https://github.com/scalableminds/webknossos/pull/7964)

### Changed
- The warning about a mismatch between the scale of a pre-computed mesh and the dataset scale's factor now also considers all supported mags of the active segmentation layer. This reduces the false posive rate regarding this warning. [#7921](https://github.com/scalableminds/webknossos/pull/7921/)
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13 changes: 11 additions & 2 deletions ...e/app/com/scalableminds/webknossos/datastore/datareaders/zarr/ZarrCompressorFactory.scala
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Expand Up @@ -4,9 +4,11 @@ import com.scalableminds.webknossos.datastore.datareaders.{
BloscCompressor,
CompressionSetting,
Compressor,
IntCompressionSetting,
NullCompressor,
StringCompressionSetting,
ZlibCompressor
ZlibCompressor,
ZstdCompressor
}

object ZarrCompressorFactory {
Expand All @@ -23,6 +25,13 @@ object ZarrCompressorFactory {
case "null" => nullCompressor
case "zlib" => new ZlibCompressor(properties)
case "blosc" => new BloscCompressor(properties)
case _ => throw new IllegalArgumentException("Compressor id:'" + id + "' not supported.")
case "zstd" => {
val level = properties.get("level") match {
case Some(IntCompressionSetting(l)) => l
case _ => throw new IllegalArgumentException("Zstd level must be int")
}
new ZstdCompressor(level, checksum = false)
}
case _ => throw new IllegalArgumentException("Compressor id:'" + id + "' not supported.")
}
}