Implement compressed segmentation #6947
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frcroth
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...nossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
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...calableminds/webknossos/datastore/datareaders/precomputed/compressedsegmentation/LICENSE.txt
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webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/ChunkReader.scala
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...calableminds/webknossos/datastore/datareaders/precomputed/PrecomputedCompressorFactory.scala
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...nossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
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| private def decompressChannel(input: Array[Int], volumeSize: Array[Int], blockSize: Array[Int]): Array[T] = { | ||
| assert(blockSize.length == 3) | ||
| val numElements = volumeSize(0) * volumeSize(1) * volumeSize(2) |
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is the order of volumeSize elements fixed? can we rely on 0,1,2 being x,y,z, and 3 being c? Could there be a time axis as well?
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The specification only describes 3d volume data, so I think it can be left like this.
...nossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
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Probably a different issue: I just tried to import |
Yes, that’s #6821 |
Co-authored-by: Norman Rzepka <[email protected]>
...calableminds/webknossos/datastore/datareaders/precomputed/PrecomputedCompressorFactory.scala
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| override def toString: String = s"compressor=$getId/dataType=${dataType.toString}" | ||
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| private def blockSizeVec = Vec3Int(x = blockSize(0), y = blockSize(1), z = blockSize(2)) |
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could blockSize be Vec3Int everywhere? (even in case class PrecomputedScale). Then the json validator would already reject it if it does not match, and we wouldn’t need the conversion here
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oh I did not know Vec3Int could be automatically parsed.
URL of deployed dev instance (used for testing):
Steps to test:
I did not find segmentation datasets with uint32 as data type
Current problems:
Segment ids are not correct. That is, the shapes that result are correct, but they do not have the right ids. Also, some segments are missing.Performance is pretty bad right nowEnsure License complianceUpdate docs: Remove wkconnect?Issues:
(Please delete unneeded items, merge only when none are left open)