[ome-users] Bug in Bio-Formats/Fiji

[David Gault (Staff)]

Hi Jacob,

I was able to test and reproduce the issue as reported with the sample file provided.The problem appears to be that the expected data block size is much larger than the available space.

The metadata appears to be read correctly and matches with the details provide, however for an expected 256*256 pixels with 1024 channels the file size does seem much smaller than would be required.
Would you be able to provide further details as to the type of image data expected within the datablock?

With Thanks,
David Gault

> On 16 Oct 2017, at 12:20, Jacob Seifert <derduxon at gmail.com> wrote:
>
> Dear OME users,
>
> I've encountered a bug while importing *.sdt (Becker & Hickl SPCImage v6.2) files:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 452MB of 6045MB (7%)
>
> java.lang.IllegalArgumentException
> at java.nio.Buffer.position(Buffer.java:244)
> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:605)
> at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:451)
> at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:597)
> at loci.formats.in.SDTInfo.<init>(SDTInfo.java:956)
> at loci.formats.in.SDTReader.initFile(SDTReader.java:393)
> at loci.formats.FormatReader.setId(FormatReader.java:1397)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
> at loci.plugins.in.Importer.showDialogs(Importer.java:140)
> at loci.plugins.in.Importer.run(Importer.java:76)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:217)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at java.lang.Thread.run(Thread.java:745)
>
>
> Bio-Formats is on version 5.7.1. A non-working file [722 kiB] is attached.
> Metadata of this file: 256x256 pixel image with fluorescence lifetime information in 1024 channels.
>
> Regards,
> Jacob
>
>
> <exc1_c1.sdt>_______________________________________________
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