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constantinpape / cluster_tools

Distributed segmentation for bio-image-analysis
MIT License
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Make 'compression' configurable when creating label-to-block-mapping #13

Closed wolny closed 5 years ago

wolny commented 5 years ago

Workaround for the following issue that occurs when trying to commit changes in paintera:

[Thread-71] INFO org.janelia.saalfeldlab.paintera.data.n5.CommitCanvasN5 - Committing canvas: 7 blocks
[Thread-71] INFO org.janelia.saalfeldlab.paintera.data.n5.CommitCanvasN5 - Finished commiting canvas
Exception in thread "Thread-71" java.lang.RuntimeException: Error while trying to persist.
    at org.janelia.saalfeldlab.paintera.data.mask.MaskedSource.lambda$persistCanvas$13(MaskedSource.java:621)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.janelia.saalfeldlab.paintera.data.mask.persist.UnableToUpdateLabelBlockLookup: Unable to update label block lookup for /paintera
    at org.janelia.saalfeldlab.paintera.data.n5.CommitCanvasN5.updateLabelBlockLookup(CommitCanvasN5.java:201)
    at org.janelia.saalfeldlab.paintera.data.mask.MaskedSource.lambda$persistCanvas$13(MaskedSource.java:610)
    ... 1 more
Caused by: java.io.IOException: Input is not in the .gz format
    at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.init(GzipCompressorInputStream.java:164)
    at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.<init>(GzipCompressorInputStream.java:137)
    at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.<init>(GzipCompressorInputStream.java:102)
    at org.janelia.saalfeldlab.n5.GzipCompression.getInputStream(GzipCompression.java:64)
    at org.janelia.saalfeldlab.n5.DefaultBlockReader.read(DefaultBlockReader.java:49)
    at org.janelia.saalfeldlab.n5.DefaultBlockReader.readBlock(DefaultBlockReader.java:87)
    at org.janelia.saalfeldlab.n5.N5FSReader.readBlock(N5FSReader.java:169)
    at org.janelia.saalfeldlab.labels.blocks.n5.LabelBlockLookupFromN5.readMap(LabelBlockLookupFromN5.kt:124)
    at org.janelia.saalfeldlab.labels.blocks.n5.LabelBlockLookupFromN5.read(LabelBlockLookupFromN5.kt:103)
    at org.janelia.saalfeldlab.paintera.data.n5.CommitCanvasN5.updateLabelBlockLookup(CommitCanvasN5.java:162)
    ... 2 more