[vtkusers] stenciling problem-- is this code thread safe?
Mark Roden
mmroden at gmail.com
Fri Feb 11 15:46:08 EST 2011
Out of curiousity, how does sample code like
http://vtk.org/gitweb?p=VTK.git;a=blob;f=Examples/GUI/Tcl/ImageTracerWidget.tcl
now work if the vtkPolyDataToImageStencil only works on lines? That
code also appears to use polys instead of lines.
On Fri, Feb 11, 2011 at 12:34 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
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>> 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://www.vtk.org/mailman/listinfo/vtkusers
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
More information about the vtkusers
mailing list