[Paraview] Resampling data in ParaView

Fri Jun 4 09:34:01 EDT 2010

Berk, Utkarsh,

Thanks a lot for your kind explanation. For now, my way of using
ParaView is almost serial-and-client-only. BUT my wish is to bring the
power of ParaView, regarding the parallelization, to the medical imaging
community. I want to make *no* modification to the original source code
of external lib, thus having an easy-to-maintain software package.

Conclusion is: Looking forward to testing your pipeline enhancements!

Deep thanks
Jerome

2010/6/4 Berk Geveci <berk.geveci at kitware.com>:
> Hi Jerome,
>
>> 2) to submit a patch to the VTK developers that modifies the current
>> implementation
>
> This is harder than you think. The current implementation is "broken"
> for a good reason. I'll try to explain.
>
> ParaView is first and foremost designed
> for distributed memory parallel computing. Its main mode of operation
> is data parallel: each process loads a subset of the whole mesh and
> filters it, for the most part, in an embarrassingly parallel fashion. One of
> the main bottlenecks (actually, THE main bottleneck) of distributed parallel
> processing is IO. We want to minimize IO whenever possible. This
> desire conflicts with the way structured data pipeline works by default.
> The structured pipeline aims to always keep data load balanced. For
> example, if I load a mesh, then extract a subset (with extract VOI) and
> then contour it, the default VTK implementation will try to first split the
> whole mesh into n (where n is the number of pieces) and then try to
> split the output of extract VOI into n. Depending on what extract VOI
> is extracting, the second partitioning may be different than the first,
> causing processes to reload different parts of data.
>
> To avoid this problem, ParaView uses a custom extent translator. However,
> this extent translator was not designed with all image filters in mind.
> Hence the problem you are seeing.
>
> If you are running only in serial mode, the problem is easy to solve.
> Change the ParaView code to use its extent translator only when running
> in parallel. However, if you are running in parallel, you cannot do this.
>
> I am working on making some changes to the VTK pipeline that will
> hopefully address this issue in the future.
>
> -berk
>
>
>
> On Thu, Jun 3, 2010 at 5:48 PM, Jérôme <jerome.velut at gmail.com> wrote:
>> Utkarsh,
>>
>> clear up a doubt for me please: Does it mean that if I want to use
>> vtkImageConstantPad filter in ParaView, I only have two solutions
>> that are
>> 1) to write vtkPVImageConstantPad that uses the extent translator
>> correctly,
>> 2) to submit a patch to the VTK developers that modifies the current
>> implementation
>>
>> Thanks again!
>>
>> Jerome
>>
>> 2010/6/3 Jérôme <jerome.velut at gmail.com>:
>>> Fine!
>>> Thanks a lot for your explanations. Then I will work on that.
>>> Do you mind if I go on this thread for eventual misunderstandings?
>>>
>>> Jerome
>>>
>>> 2010/6/3 Utkarsh Ayachit <utkarsh.ayachit at kitware.com>:
>>>> Jerome,
>>>>
>>>> The VTK class has the trick to override the extent-translator which is
>>>> what does-what-it-does in ParaView. ParaView by default overrides the
>>>> extent translator with vtkPVExtentTranslator which uses the original
>>>> data exetent information for partitioning and that's what messes such
>>>> fancy pipelines up. The filer can explicitly override ParaView's
>>>> behavior. So to answer, no, there's nothing on ParaView side that
>>>> needs to be added to support changing of extents it is in the
>>>> pipeline.
>>>>
>>>> Utkarsh
>>>>
>>>> On Thu, Jun 3, 2010 at 2:24 PM, Jérôme <jerome.velut at gmail.com> wrote:
>>>>> Hi Utkarsh,
>>>>>
>>>>> Thanks for your tips. I will take a look around this class. Though I have
>>>>> a question: This is a VTK class, and I don't have problem in stand-alone
>>>>> VTK applications. If I have to change something in VTK classes, it means
>>>>> that I will have duplicated filters, the native VTK ones and the modified
>>>>> of mine... Don't you think there something on ParaView-side to do?
>>>>>
>>>>> Thanks again and best regards,
>>>>> Jerome
>>>>>
>>>>> 2010/6/3 Utkarsh Ayachit <utkarsh.ayachit at kitware.com>:
>>>>>> Jerome,
>>>>>>
>>>>>> You may want to look at VTK/Hybrid/vtkImageDataLIC2D.cxx to see how it
>>>>>> plays tricks with the extent-translator to generate images with larger
>>>>>> extent when magnification > 1.
>>>>>>
>>>>>> Utkarsh
>>>>>>
>>>>>> On Thu, Jun 3, 2010 at 5:02 AM, Jérôme <jerome.velut at gmail.com> wrote:
>>>>>>> Finally, I found a bug opened 6 months ago:
>>>>>>>   http://www.paraview.org/Bug/view.php?id=10125
>>>>>>> I added a note. I hope that it will interest some PV gurus
>>>>>>>
>>>>>>> Jerome
>>>>>>>
>>>>>>> 2010/6/2 Jérôme <jerome.velut at gmail.com>:
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I fill very surprised that *nobody* has to resample some data inside
>>>>>>>> ParaView. Several threads deal with enabling some VTK filters in
>>>>>>>> ParaView that actually change the extent of the input image (just as
>>>>>>>> vtkImageResample), but when the output extent is higher that input,
>>>>>>>> there is a strange behaviour. Sorry for being lazy: the problem was
>>>>>>>> described in the following threads.
>>>>>>>>   http://www.paraview.org/pipermail/paraview/2010-May/017309.html
>>>>>>>>   http://www.paraview.org/pipermail/paraview/2009-October/014306.html
>>>>>>>>   http://www.paraview.org/pipermail/paraview/2009-April/011945.html
>>>>>>>>
>>>>>>>> Please, tell me if I am doing something wrong in the XML, if I am
>>>>>>>> stupid, if this is a known limitation of ParaView, if I am not sending
>>>>>>>> to the right mailing list, if [put your own proposition].
>>>>>>>>
>>>>>>>> Thanks for all, and best regards.
>>>>>>>> Jerome
>>>>>>>>
>>>>>>>> PS: you can find the incriminated XML files here:
>>>>>>>> http://github.com/jeromevelut/Peavip . Beware of the Spline Filter,
>>>>>>>> another pending request has been sent.
>>>>>>>>
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>>>>>>
>>>>>
>>>>
>>>
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