[ome-users] Bio-formats - Bug while parsing Micro-Manager metadata

[Simone Leo]

Hi Stephane,

Thanks for reporting the bug. After initial investigation, this appears
to be tied to an incorrect handling of nested arrays in FrameKey
entries. I have opened a Trello card for it at
https://trello.com/c/iaXfpx63, which can be used to track the issue.

Best,

Simone

On 06/04/2017 16:45, Stephane Dallongeville wrote:
> Dear Bio-formats team,
>
> We encounter a problem (verified on last Bio-Formats version) when we
> try to load a Micro-Manager generated dataset with the metadata text file.
> I attached one of the image of the dataset (don't need to provide the
> whole dataset) and the problematic metadata.txt file.
> Here's the error log we obtain when we try to open the image with the
> metadata.txt file in the same folder :
>
> java.lang.StringIndexOutOfBoundsException: String index out of range: -2
>     at java.lang.String.substring(String.java:1911)
>     at
> loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:808)
>
>     at
> loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)
>
>     at
> loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)
>     at loci.formats.FormatReader.setId(FormatReader.java:1397)
>     at
> plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:496)
>
>     at icy.file.Loader.internalLoadSingle(Loader.java:3101)
>     at icy.file.Loader.loadSequences(Loader.java:2707)
>     at icy.file.Loader$7.run(Loader.java:2371)
>     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>     at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>
>     at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>
>     at java.lang.Thread.run(Thread.java:745)
>
>
> If we remove the metadata.txt file the problem disappears.
> Hope it helps to resolve the issue :)
>
> Best,
>
>
>
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