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

David Gobbi david.gobbi at gmail.com
Fri Feb 11 16:24:05 EST 2011 

Ah, it looks like TestImageTracerWidget.cxx uses slices that
aren't parallel to the XY plane... so it actually has to use the
old extrusion method to prepare the data.

 - David


On Fri, Feb 11, 2011 at 1:57 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> I was recommending that you visualize the contours as polydata,
> so telling me that you are still getting blank images doesn't help
> to move things forward.
>
> PolyDataToImageStencil still works on polys. It has two modes:
> it can be given a closed polyhedral surface (like before) or,
> in VTK 5.8 and 5.9, it can be given a set of polyline contours.
> But if its input contains any polys, then it will ignore the polylines.
> And if given a set of polys that do not form a closed surface, it
> will usually not work (this depends on the orientation of the polys).
> Given a single, flat poly it will never work, if given polys the polys
> must define an enclosed volume.
>
> The vtkImageTracer widget has not been updated recently, so
> it still uses extrusion in order to generate a surface, instead of
> using the more efficient contour-to-stencil conversion.
>
> The contours should be closed and connected, which they should
> be if they are generated from polygon edges, but vtkCleanPolyData
> can be used as further insurance.  An example of contour use is
> Hybrid/Testing/Tcl/TestImageStencilWithPolydata.tcl
>
> But I've gone ahead and merged a patch for the vtkLinearExtrusion
> multithreading bug.  I'd prefer if you continued to diagnose the
> contour issue and get it working that way, but that's up to you.
>
>  - David
>
>
> On Fri, Feb 11, 2011 at 1:34 PM, Mark Roden <mmroden at gmail.com> wrote:
>> Hi David,
>>
>> Yes, I'm feeding these things into a visualizer.  It's the same code
>> path as when I was using 5.6, in that it's going right into a mapper
>> to an actor to a renderer.  I'm getting blank images.
>>
>> I'm wondering if it could be easier to avoid this extra filter (that
>> seems to have some kind of angle threshold?) and just redo the gdcm
>> poly reader to report both polys and lines, and then blank the polys
>> if necessary for the stenciling code.
>>
>> rtstructs are just a series of points that are supposed to be linearly
>> connected.  right now, the code to feed them into the polys array
>> looks like:
>>
>>
>>    vtkCellArray *polys = vtkCellArray::New();
>>    for(unsigned int i = 0; i < nitems; ++i){//nitems = number of
>> closed contour polygons
>>      ....
>>      for(unsigned int i = 0; i < npts * 3; i+=3)
>>        {
>>        float x[3];
>>        x[0] = pts[i+0];
>>        x[1] = pts[i+1];
>>        x[2] = pts[i+2];
>>        vtkIdType ptId = newPts->InsertNextPoint( x );
>>        ptIds[i / 3] = ptId;
>>        }
>>      // Each Contour Data is in fact a Cell:
>>      vtkIdType cellId = polys->InsertNextCell( npts , ptIds);
>>   }
>> Could you point me to some sample code I can use to construct the
>> lines necessary to make your filter work, as opposed to the polys that
>> the reader is currently producing?
>>
>>
>>
>> On Fri, Feb 11, 2011 at 12:14 PM, David Gobbi <david.gobbi at gmail.com> wrote:
>>> A better approach would be to visualize the contours to make
>>> sure there's nothing wrong with them.  Just feed them into a
>>> vtkDataSetMapper, add that mapper to a vtkActor, and add that
>>> to your renderer.  If they don't look right, then do the same for the
>>> polygons. You need to know what kind of input you are feeding into
>>> vtkPolyDataToImageStencil before you start worrying about the output.
>>>
>>> On Fri, Feb 11, 2011 at 1:01 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>> whoops.  Thanks for that.
>>>>
>>>> Now theLines has some information in it, although more than I think it should.
>>>>
>>>> Still not showing up in my displays, though, whereas it was in the 5.6 version.
>>>>
>>>> Is there a way to quickly walk through the contents of vtkImageData to
>>>> see if there's anything there produced by the stenciling?  I'm
>>>> wondering if something's broken in the visualization code.
>>>>
>>>> On Fri, Feb 11, 2011 at 11:57 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>> I gotta ask... did you call theEdges.Update() before checking the output?
>>>>>
>>>>> On Fri, Feb 11, 2011 at 12:49 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>> Yeah, that doesn't work.
>>>>>>
>>>>>>        vtkCellArray thePolys = data.GetPolys();
>>>>>>        vtkCellArray theStrips = data.GetStrips();
>>>>>>        vtkCellArray theLines = data.GetLines();
>>>>>>
>>>>>>        vtkFeatureEdges theEdges = new vtkFeatureEdges();
>>>>>>        theEdges.BoundaryEdgesOn();
>>>>>>        theEdges.ManifoldEdgesOn();
>>>>>>        theEdges.NonManifoldEdgesOn();
>>>>>>        theEdges.FeatureEdgesOn();
>>>>>>        theEdges.SetInput(data);
>>>>>>        vtkPolyData theEdgeData = theEdges.GetOutput();
>>>>>>
>>>>>>        thePolys = theEdgeData.GetPolys();
>>>>>>        theStrips = theEdgeData.GetStrips();
>>>>>>        theLines = theEdgeData.GetLines();
>>>>>>
>>>>>> thePolys, theStrips, and theLines are all zero-sized once
>>>>>> theFeatureEdges filter is run, but thePolys has 25 points (for my test
>>>>>> data) prior to running.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Feb 11, 2011 at 11:37 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>>> You could try vtkFeatureEdges. There is probably a better filter for
>>>>>>> the job, but I don't know.
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Feb 11, 2011 at 12:25 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>>>> OK, so it looks like everything's coming back as polys instead of
>>>>>>>> lines.  What's the best way to proceed then, modify the reader to get
>>>>>>>> just lines, or is there some way to convert from the polys to lines?
>>>>>>>>
>>>>>>>> On Fri, Feb 11, 2011 at 11:12 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>>>>> Just verify that the vtkGDCMPolyDataReader contains no polygons, i.e.
>>>>>>>>> get its output and call output.GetPolys() and output.GetStrips().
>>>>>>>>> Both of these should be null, because a single polygon or strip in the
>>>>>>>>> polydata will keep the contour code from working.  The output of
>>>>>>>>> GetLines() should, of course, not be null, since that is what
>>>>>>>>> vtkPolyDataToImageStencil will use to create the stencil.
>>>>>>>>>
>>>>>>>>>  - David
>>>>>>>>>
>>>>>>>>> On Fri, Feb 11, 2011 at 12:05 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>>>>>> So in this code, which is using a vtkPolyData 'data' that is a series
>>>>>>>>>> of xy contours along the z axis, as restored by the
>>>>>>>>>> vtkGDCMPolyDataReader (and working in 5.6):
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>        //vtk 5.9 no longer requires linear extrusion beforehand
>>>>>>>>>>        //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.SetInput(data);
>>>>>>>>>>        pol2Stenc.SetInformationInput(binaryOrgan);
>>>>>>>>>>        pol2Stenc.Update();
>>>>>>>>>>        vtkImageStencilData pol2StencOutput = pol2Stenc.GetOutput();
>>>>>>>>>>
>>>>>>>>>>        vtkImageStencil stencil = new vtkImageStencil();
>>>>>>>>>>        stencil.SetInput(binaryOrgan);
>>>>>>>>>>        stencil.ReverseStencilOn();
>>>>>>>>>>        stencil.SetStencil(pol2StencOutput);
>>>>>>>>>>        stencil.Update();
>>>>>>>>>>
>>>>>>>>>>        final vtkImageData stencilOutput = stencil.GetOutput();
>>>>>>>>>>        final vtkImageData imageToKeep = new vtkImageData();
>>>>>>>>>>        imageToKeep.DeepCopy(stencilOutput);
>>>>>>>>>>        stencilOutput.Delete();
>>>>>>>>>>
>>>>>>>>>> The result is a blank image.  Is there a call I'm missing here?
>>>>>>>>>>
>>>>>>>>>> On Fri, Feb 11, 2011 at 11:00 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>>>>>>> The vtkPolyDataToImageStencil in VTK 5.8 and 5.9 can take a polyline
>>>>>>>>>>> contour or a stack of contours as input and create a stencil from
>>>>>>>>>>> that.  Each polylines should lie in an XY plane (though they can be at
>>>>>>>>>>> any Z position).  This will not work with a polygon; a polyline is
>>>>>>>>>>> required.
>>>>>>>>>>>
>>>>>>>>>>>  - David
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Feb 11, 2011 at 11:51 AM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>>>>>>>> Hi David,
>>>>>>>>>>>>
>>>>>>>>>>>> How should the stenciling be done in vtk 5.9 then?  If I remove the
>>>>>>>>>>>> linear extrusion, no masks are produced.
>>>>>>>>>>>>
>>>>>>>>>>>> This is exciting-- I can now use the vtkSmartVolumeMapper, which I've
>>>>>>>>>>>> been drooling over ever since it was introduced!
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Mark
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Feb 11, 2011 at 10:39 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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>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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