[vtkusers] How to prevent out-of-memory crash with vtkImageReader from Java

[Marco Sambin]

Hi Seb,

first of all, thanks for your feedback.

I have taken a look at the C++ code of vtkImageReader: it seems to me that
main allocation happens inside ExecuteDataWithInformation() method, which
in turn calls vtkImageData::AllocateScalars(), which in turn
calls vtkDataArray::CreateDataArray(), which finally I think ends up
calling ::New() on the typed data array (probably, vtkUnsignedShortArray in
my case).

If I were to write my own image reader, for instance, I am not sure how I
could detect eventual out-of-memory errors, since they would actually
happen inside other VTK classes. Maybe some try-catch blocks in my own
image reader may help me?
Any suggestion would be greatly appreciated.

I am looking forward to hearing from you.
Thanks and best regards,

Marco Sambin


On Wed, Oct 15, 2014 at 4:30 PM, Sebastien Jourdain <
sebastien.jourdain at kitware.com> wrote:

> Hi Marco,
>
> I don't have the answer but if there is no solution as today, maybe adding
> another method on the reader that could first validate that enough memory
> is available, might be an option. Specially in Java when such call make the
> JVM crash.
>
> That change will need to happen on the C++ side. But at that point I'm not
> sure how to check that on the C++ side either. Maybe Berk, Dave or Brad
> might have some insight.
>
> Thanks,
>
> Seb
>
>
>
> On Wed, Oct 15, 2014 at 3:04 AM, Marco Sambin <m.sambin at gmail.com> wrote:
>
>> Hi all.
>> In my VTK-based Java application, I am reading a "raw volume file"
>> (containing a set of CT slices) through some Java code looking like this:
>>
>> [...]
>> vtkImageReader imageReaderVTK =  new vtkImageReader();
>> imageReaderVTK.FileLowerLeftOn();
>> imageReaderVTK.SetFileDimensionality(3);
>> imageReaderVTK.SetFileName(curRawVolFile.getAbsolutePath());
>> imageReaderVTK.SetDataExtent(0, sliceCols - 1,
>>                       0, sliceRows - 1,
>>                       0, numOfUsedImages - 1);
>> imageReaderVTK.SetDataSpacing(xSpacing, ySpacing, zSpacing);
>> imageReaderVTK.SetDataOrigin(0.0, 0.0, 0.0);
>> imageReaderVTK.SetDataScalarTypeToUnsignedShort();
>> imageReaderVTK.SetDataByteOrderToBigEndian();
>>
>> // The following call may cause a process crash due to out-of-memory
>> imageReaderVTK.UpdateWholeExtent();
>> [...]
>>
>> I am then passing this volume to a vtkImagePlaneWidget for some reslicing.
>>
>> As the last comment (in the code fragment above) suggests, in some cases
>> I get a crash of the JVM process, due to the fact the reader goes out of
>> memory while actually reading and allocating the whole volume in memory.
>> This especially happens when using a 32-bit JRE.
>> I understand that I cannot read a huge volume in memory if just a small
>> amount of memory is available to the process, but my question is:
>> is there a way to manage "more gracefully" this out-of-memory from Java
>> code, in such a way to be able to inform the user that "Not enough memory
>> is available to read this volume", instead of causing a JVM crash?
>>
>> I am using VTK 6.1.0.
>>
>> Thanks for any hint/suggestion about this topic.
>>
>> Best regards,
>>
>> Marco
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/vtkusers
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/vtkusers/attachments/20141022/3845fad6/attachment.html>