[vtkusers] stenciling problem-- is this code thread safe?
Mark Roden
mmroden at gmail.com
Fri Feb 11 17:54:26 EST 2011
Ah, I will almost definitely have multiple contours per slice. Thanks
for the warning, I'll go back to the old way for now.
On Fri, Feb 11, 2011 at 2:43 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> Yeah, it should be Lasso. It looked just a little wrong to me but
> if you hadn't mentioned it to me I wouldn't have checked. I'm
> pretty sure Kitware will allow me to fix my typo before VTK 5.8
> is finalized.
>
> Good luck. But before you try Lasso, I do have one caveat
> about it, too. It only allows one contour per slice, and I
> suspect that if you are reading contours from DICOM files,
> there is the possibility that you will have multiple contours
> per slice. (You're always welcome to dig into the VTK
> classes and add features to fit your requirements).
>
> - David
>
>
> On Fri, Feb 11, 2011 at 3:24 PM, Mark Roden <mmroden at gmail.com> wrote:
>> Hi David,
>>
>> That's not working either.
>>
>> I'm going to have to really debug what's going on here. I literally
>> just swapped out libraries, and what was getting displayed before is
>> now not getting displayed at all. I just tried the lasso tool (is it
>> lassoo or lasso? wikipedia redirects lassoo to lasso) and that didn't
>> change anything. I might have something busted on my end that was
>> exploiting some corner case in 5.6 that's now gone in 5.9.
>>
>> Thanks,
>> Mark
>>
>> On Fri, Feb 11, 2011 at 1:56 PM, David Gobbi <david.gobbi at gmail.com> wrote:
>>> I should add: vtkLassooStencilSource is not only much more
>>> efficient than vtkPolyDataToImageStencil, but it is also much
>>> more robust. Internally it is simpler and has fewer heuristics.
>>>
>>> - David
>>>
>>>
>>> On Fri, Feb 11, 2011 at 2:48 PM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>> The old code shouldn't break, it didn't break any of the
>>>> regression tests at least. To be safe, you should be using
>>>> vtkTransformToPolyDataFilter to add a shift to the extruded
>>>> data, just like the TestImageTracerWidget.
>>>>
>>>> Your other option is to use vtkLassoStencilSource (new in VTK 5.8)
>>>> instead of vtkPolyDataToImageStencil. It requires you to build
>>>> your own contours (it takes a list of points as input) but it is more
>>>> efficient than vtkPolyDataToImageStencil and it can take x-aligned
>>>> and y-aligned contours as well as z-aligned. It has a
>>>> SetSliceOrientation() method to allow you to set the orientation.
>>>>
>>>> - David
>>>>
>>>>
>>>> On Fri, Feb 11, 2011 at 2:33 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>>> I guess the question is why the 5.6 method doesn't work with 5.9, if
>>>>> the extrusion/polydatatostencil/stencil pipeline should be good-- ie,
>>>>> if I have contours drawn along the x plane, I'll need this
>>>>> non-z-stacking approach to work (and I do have such contours). Our
>>>>> app allows users to draw their contours on any plane, so the z-aligned
>>>>> contour assumption isn't entirely useful to me.
>>>>>
>>>>> It looks like there's a noop happening somewhere, as if the something
>>>>> in that pipeline just decided that because there are only polys (or
>>>>> something similar), it's not going to do the work. If polys are still
>>>>> a valid input, then why should the old code break?
>>>>>
>>>>> On Fri, Feb 11, 2011 at 1:24 PM, David Gobbi <david.gobbi at gmail.com> wrote:
>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Powered by www.kitware.com
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>>>>>>>>>>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>
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>>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
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>>>
>>
>
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