[ome-devel] in-memory reading

[Manuel Stritt]

Hi Roger,

thanks a lot for this detailed analysis, I highly appreciate this!

Regards,
Manuel


On 01/09/17 15:14, Roger Leigh wrote:
>
>> On 01/09/17 10:00, Manuel Stritt wrote:
>>
>>> Dear all,
>>>
>>> I'm trying to use the in-memory reading method as documented here:
>>>
>>> https://docs.openmicroscopy.org/bio-formats/5.6.0/developers
>>> /in-memory.html
>>>
>>>
>>> in combination with a NDPI reader + BufferedImageReader:
>>>
>>
>> Making this into a compilable example, the stack trace is this:
>>
> [...]
>
> Dear Manuel,
>
> I've written another two small examples as modifications to test exactly
> where the failure lies.
>
> testfile replaces the in-memory I/O with regular file I/O.  This works
> correctly, with BufferedImageReader.
>
> testplain retains the in-memory I/O but replaces BufferedImageReader
> with regular openBytes.  This fails:
>
> Reading file into memory from disk...
> 3544235 bytes read.
> size reader: 3968 x4864
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>         at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:57)
>         at java.nio.ByteBuffer.allocate(ByteBuffer.java:335)
>         at loci.common.ByteArrayHandle.setLength(ByteArrayHandle.java:111)
>         at loci.common.ByteArrayHandle.seek(ByteArrayHandle.java:180)
>         at
> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
>         at
> loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurbo
> ServiceImpl.java:303)
>         at
> loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurbo
> ServiceImpl.java:235)
>         at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:191)
>         at loci.formats.FormatReader.openBytes(FormatReader.java:886)
>         at testplain.main(testplain.java:43)
>
> It's clear that the NDPI reader is behaving differently with the in
> memory stream vs a regular file stream.
>
> This has been recorded here:
> https://trello.com/c/C4v0GnWv/185-ndpi-in-memory-reading
>
>
> Regards,
> Roger
>
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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>
>

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