[vtkusers] stenciling problem-- is this code thread safe?

[David Gobbi]

That could indicate a problem with static methods, since SetInstance()
is static, but I don't know the Java wrappers well enough to know what
vtkId is for.  Perhaps vtkId it is vtkJava-specific "this" member and
the wrappers are incorrectly using it inside a static method.

I've CC'd Mathieu in case he might have some insight.

 - David


On Fri, Feb 11, 2011 at 11:39 AM, Mark Roden <mmroden at gmail.com> wrote:
> wait, never mind!  I had some issues with vtk strings, but it appears
> that this line:
>
> outWin.SetInstance(outWin);
>
> is now deprecated or something, because having that line active in this snippet:
>
>            vtkFileOutputWindow outWin = new vtkFileOutputWindow();
>            outWin.SetInstance(outWin);
>            outWin.SetFileName("MVSVTKViewer.log");
>
> throws this exception:
>
> Exception in thread "main" java.lang.NoSuchFieldError: vtkId
>        at vtk.vtkOutputWindow.SetInstance_3(Native Method)
>        at vtk.vtkOutputWindow.SetInstance(vtkOutputWindow.java:45)
>        at com.mvs.viewer.Application.main(Application.java:63)
>
> But that's a different issue (bug?)
>
> On Fri, Feb 11, 2011 at 10:35 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>> If you are reporting the vtkLinearExtrusionFilter, I already did.
>>
>> On Fri, Feb 11, 2011 at 11:31 AM, Mark Roden <mmroden at gmail.com> wrote:
>>> Hi David,
>>>
>>> Unfortunately,  the current vtk master branch is seriously broken in
>>> its java wrappings.  I'm putting together a bug report now...
>>>
>>> Thanks,
>>> Mark
>>>
>>> On Fri, Feb 11, 2011 at 10:09 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>> I should add: with the current VTK master and release branches,
>>>> vtkPolyDataToImageStencil no longer requires vtkLinearExtrusionFilter
>>>> to be used beforehand.  So you could try that.
>>>>
>>>>  - David
>>>>
>>>>
>>>> On Fri, Feb 11, 2011 at 11:06 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>> I was doubtful about the global memory, but I looked through the
>>>>> filters just to be sure.  And guess what I found... here is some
>>>>> highly suspect code in vtkLinearExtrusionFilter:
>>>>>
>>>>> double *vtkLinearExtrusionFilter::ViaNormal(double x[3], vtkIdType id,
>>>>>                                           vtkDataArray *n)
>>>>> {
>>>>>  static double xNew[3], normal[3];
>>>>>  int i;
>>>>>
>>>>>  n->GetTuple(id, normal);
>>>>>  for (i=0; i<3; i++)
>>>>>    {
>>>>>    xNew[i] = x[i] + this->ScaleFactor*normal[i];
>>>>>    }
>>>>>
>>>>>  return xNew;
>>>>> }
>>>>>
>>>>> Code like the above is definitely going to cause thread problems.
>>>>> And this isn't the only place in that class where code like this appears.
>>>>>
>>>>> Yikes!
>>>>>
>>>>>  - David
>>>>>
>>>>>
>>>>> On Fri, Feb 11, 2011 at 10:46 AM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>> What I mean is, I have a vtkPolyData that has been DeepCopied and a
>>>>>> vtkImageData that is binary and distinct from all other data.
>>>>>>
>>>>>> When I call the previously listed code with multiple threads (each
>>>>>> with their own polydata and binary image to fill in), the result is
>>>>>> generally a very garbled image.  If I call from a single thread in
>>>>>> series, one for each polydata/image pair, then everything works out
>>>>>> fine.
>>>>>>
>>>>>> So it seems to me that something in the above series isn't thread
>>>>>> safe.  Each thread is declaring its own local objects, but is there
>>>>>> some global memory that's being used or accessed here?
>>>>>>
>>>>>> On Fri, Feb 11, 2011 at 9:23 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>>> Hi Mark,
>>>>>>>
>>>>>>> Explain in more detail what you mean by "call from multiple threads".
>>>>>>> VTK is, in general, not thread safe and you cannot call Update() on
>>>>>>> a filter from more than one thread.  Each thread needs to have its own
>>>>>>> set of filters.  And in general, you cannot feed a data object into more
>>>>>>> than one thread, because even simple methods like GetBounds() are
>>>>>>> not thread safe.
>>>>>>>
>>>>>>> When using VTK from multiple threads, it is necessary to apply
>>>>>>> extreme caution.
>>>>>>>
>>>>>>>  - David
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Feb 11, 2011 at 10:00 AM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> This code does not have threads enabled in vtk 5.6.1 (the code is in Java):
>>>>>>>>
>>>>>>>>        vtkLinearExtrusionFilter extruder = new vtkLinearExtrusionFilter();
>>>>>>>>        extruder.SetInput(data);
>>>>>>>>        extruder.SetVector(0, 0, spacing[2]);
>>>>>>>>        extruder.Update();
>>>>>>>>        vtkPolyData extruderOutput = extruder.GetOutput();
>>>>>>>>
>>>>>>>>        vtkPolyDataToImageStencil pol2Stenc = new vtkPolyDataToImageStencil();
>>>>>>>>        pol2Stenc.SetTolerance(0);
>>>>>>>>        pol2Stenc.SetInput(extruderOutput);
>>>>>>>>        pol2Stenc.SetInformationInput(binaryOrgan);
>>>>>>>>        pol2Stenc.Update();
>>>>>>>>        vtkImageStencilData pol2StencOutput = pol2Stenc.GetOutput();
>>>>>>>>
>>>>>>>>        // This is where the memory leak is!!!!
>>>>>>>>        vtkImageStencil stencil = new vtkImageStencil();
>>>>>>>>        stencil.SetInput(binaryOrgan);
>>>>>>>>        stencil.ReverseStencilOn();
>>>>>>>>        stencil.SetStencil(pol2StencOutput);
>>>>>>>>        stencil.Update();
>>>>>>>>
>>>>>>>>        // We're doing this because of an email to Mark
>>>>>>>>        // that says this will fix our memory issues
>>>>>>>>        final vtkImageData stencilOutput = stencil.GetOutput();
>>>>>>>>        final vtkImageData imageToKeep = new vtkImageData();
>>>>>>>>        imageToKeep.DeepCopy(stencilOutput);
>>>>>>>>        stencilOutput.Delete();
>>>>>>>>
>>>>>>>> When I try to call this code from multiple threads (ie, to create the
>>>>>>>> stencils for multiple organs), Bad Things happen, as in, the data are
>>>>>>>> entirely corrupted.  Is this code thread safe?
>>>>>>>>
>>>>>>>> Mark
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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>