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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


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]

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

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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