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Ticket #250 (closed defect: fixed)

Opened 2008-02-27T17:25:19-06:00

Last modified 2008-02-28T12:52:22-06:00

Bio-Rad reader throws StringIndexOutOfBoundsException with some XML fragments

Reported by:	curtis	Owned by:	melissa
Priority:	critical	Milestone:
Component:	bio-formats	Severity:	fatal
Keywords:		Cc:
Blocked By:		Blocking:

Description

BioRadReader currently uses error-prone string parsing to extract information from lse.xml files. This logic needs to be rewritten to use SAX instead.

curtis@monk:~$ showinf data/biorad/erica/2-4827_30/2-4827_30_raw.pic 
Checking file format [Bio-Rad PIC]
Initializing reader
        Reading image dimensions
        Reading notes
        Reading color table
        Populating metadata
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -13
        at java.lang.String.substring(String.java:1768)
        at loci.formats.in.BioRadReader.initFile(BioRadReader.java:839)
        at loci.formats.FormatReader.setId(FormatReader.java:633)
        at loci.formats.FormatHandler.setId(FormatHandler.java:136)
        at loci.formats.ImageReader.setId(ImageReader.java:563)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:229)
        at loci.formats.tools.ImageInfo.main(ImageInfo.java:624)

Change History

comment:1 Changed 2008-02-28T12:52:22-06:00 by melissa

Status changed from new to closed
Resolution set to fixed

r3744