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Task #12356 (closed)

Opened 5 years ago

Closed 5 years ago

Bug: Memoizer NPE for some CZI files

Reported by:	jamoore	Owned by:
Priority:	blocker	Milestone:	5.0.3
Component:	General	Version:	5.0.2
Keywords:	memoizer	Cc:	bramalingam, fs@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

2014-06-02 09:58:59,254 WARN  [                   loci.formats.Memoizer] (l.Server-7) deleted invalid memo file: /repositories/omero_reference/BioFormatsCache/repositories/omero_reference/ManagedReposit
ory/jamoore_154/2014-05/28/08-31-54.935/.Image 17-24hpf-46hpf.czi.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException
Serialization trace:
indexIntoPlanes (loci.formats.in.ZeissCZIReader)
readers (loci.formats.ImageReader)
reader (loci.formats.ChannelFiller)
reader (loci.formats.ChannelSeparator)
        at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:626) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.read(DefaultArraySerializers.java:338) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.read(DefaultArraySerializers.java:293) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221) ~[kryo.jar:na]
        at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:626) ~[kryo.jar:na]
        at loci.formats.Memoizer$KryoDeser.loadReader(Memoizer.java:137) ~[formats-bsd.jar:na]
        at loci.formats.Memoizer.loadMemo(Memoizer.java:646) [formats-bsd.jar:na]
        at loci.formats.Memoizer.setId(Memoizer.java:471) [formats-bsd.jar:na]
        at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:51) [romio.jar:na]
        at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73) [romio.jar:na]
        at ome.io.bioformats.BfPixelBuffer.close(BfPixelBuffer.java:135) [romio.jar:na]
        at omeis.providers.re.Renderer.close(Renderer.java:870) [rendering.jar:na]
        at ome.services.RenderingBean.closeRenderer(RenderingBean.java:1596) [server.jar:na]
        at ome.services.RenderingBean.close(RenderingBean.java:231) [server.jar:na]

References

Change History (4)

comment:1 Changed 5 years ago by jamoore

Note: #12083 has another Memoizer NPE in case they are related.

comment:2 Changed 5 years ago by jamoore

Summary changed from Bug: Memoizer NPE on 700GB CZI to Bug: Memoizer NPE for some CZI files

Same problem seen by Jason:

Go to gretzky

Login as user-1

Project = 27-05-14 czi Dataset: 7405

With this image, which is not large x-y dims, scrolling through Z is very slow-- ~2sec/plane. However, creating a MaxIntProj? is pretty good performance.

Not sure if this is know, expected, or even fixable.

which should be much easier to test:

omero@gretzky:/nightshade/OMERO/omero-c6100-dec-5-2013-valuable/OMERO-merge-develop-FS/ManagedRepository$ ls -ltradh user-1_8/2014-05/27/09-37-19.566/Experiment-973.czi
-rw-r--r-- 1 omero omero 28M 2014-05-27 09:37 user-1_8/2014-05/27/09-37-19.566/Experiment-973.czi

comment:3 Changed 5 years ago by pwalczysko

Please note that this image is currently just on Gretzky. The migration to octopus will proceed in such a way, that this image is not taken automatically to octopus.
To find the images easier, note that the name of the Dataset (7405) matches the QA folder on Apache, if reimport is needed.

comment:4 Changed 5 years ago by jamoore

Resolution set to fixed
Status changed from new to closed

PR opened: https://github.com/openmicroscopy/bioformats/pull/1143

Note: #12083 is independent of Memoizer and happens on new ImageReader().setId() as well.

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