Ticket #83 (closed defect: fixed)

Opened 13 years ago

Last modified 13 years ago

ArrayIndexOutOfBoundsException in TIFF metadata parsing

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


curtis@monk:~/data/tiff/steve$ showinf RBDGFP_24hrs_filter1_tap300_z5_int4_C1.tiff 
Checking file format [Tagged Image File Format]
Initializing reader
        Reading IFDs
        Populating metadata
        Checking comment style
        Found OME-TIFF: parsing OME-XML
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2
        at loci.formats.in.TiffReader.initStandardMetadata(TiffReader.java:189)
        at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:84)
        at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:819)
        at loci.formats.FormatReader.getPixelType(FormatReader.java:369)
        at loci.formats.ImageReader.getPixelType(ImageReader.java:236)
        at loci.formats.FormatTools.testRead(FormatTools.java:228)
        at loci.formats.ImageReader.testRead(ImageReader.java:517)
        at loci.formats.ImageReader.main(ImageReader.java:620)

Change History

comment:1 Changed 13 years ago by melissa

  • Status changed from new to closed
  • Resolution set to fixed

This is actually a bug in how WiscScan writes OME-TIFF files - it produces files with one OME-XML block per IFD, where each block has SizeZ = SizeT = 1. I added a hack to the OME-TIFF handler (r2504) which sets SizeT to the number of images if more than one OME-XML block is present.

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