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Task #10485 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

Bug: ND2Reader stack overflow in iterateIn

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	major	Milestone:	OMERO-4.4.7
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	chrisr@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	Bugs Fixing

Description

From QA#4932 and http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-February/003582.html

Files uploaded were "MIX 1 FITC 200MS.nd2" (works for me with current dev_4_4) and "228 and 340.nd2" (fails):

Looks like a bug with the recursion here--it recurses into iterateIn until the stack overflows.

Checking file format [Nikon ND2]
Initializing reader
Searching for blocks
Parsing block 'ND2 FILE SIG' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Exception in thread "main" java.lang.StackOverflowError
        at java.nio.charset.Charset.atBugLevel(Charset.java:249)
        at java.nio.charset.CharsetDecoder.<init>(CharsetDecoder.java:177)
        at java.nio.charset.CharsetDecoder.<init>(CharsetDecoder.java:209)
        at sun.nio.cs.UTF_8$Decoder.<init>(UTF_8.java:64)
        at sun.nio.cs.UTF_8$Decoder.<init>(UTF_8.java:62)
        at sun.nio.cs.UTF_8.newDecoder(UTF_8.java:49)
        at sun.nio.cs.StreamDecoder.<init>(StreamDecoder.java:211)
        at sun.nio.cs.StreamDecoder.forInputStreamReader(StreamDecoder.java:50)
        at java.io.InputStreamReader.<init>(InputStreamReader.java:83)
        at loci.common.RandomAccessInputStream.findString(RandomAccessInputStream.java:288)
        at loci.common.RandomAccessInputStream.findString(RandomAccessInputStream.java:214)
        at loci.common.RandomAccessInputStream.readCString(RandomAccessInputStream.java:384)
        at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1489)
        at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1526)
[iterateIn repeated 1010 times]

References

Change History (4)

comment:1 Changed 11 years ago by rleigh

Component changed from from QA to Bio-Formats
Priority changed from minor to major

comment:2 Changed 11 years ago by mlinkert

Owner changed from mlinkert-x to mlinkert

comment:3 Changed 11 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Fixed with: https://github.com/openmicroscopy/bioformats/pull/408

comment:4 Changed 11 years ago by jmoore

Milestone changed from Unscheduled to OMERO-4.5
Sprint set to Bugs Fixing

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