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

[Stephane Dallongeville]

Hi Simone,

Thanks for your response and for the tracking link, we are not in a 
hurry about this problem, just wanted to report it :)

Best,

- Stephane

Le 07/04/2017 à 15:44, Simone Leo a écrit :
> 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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>>
>
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