[vtkusers] streaming vtkMarchingCubes?
Dominik Szczerba
dominik at itis.ethz.ch
Wed Jul 29 12:06:43 EDT 2009
I do set the contour value in my code, only forgot to add the line to
the cited code.
Removing Update and UpdateWholeExtent makes no difference.
So you are suggesting that by some reason I keep appending the outputs.
Well, first off, I run it only once. But even if that may be not true by
some bug, how will you explain that on the other PC this does not happen
and I get one connected surface mesh?
-- Dominik
Bill Lorensen wrote:
> The test_cubes.vtk looks like it is the output of 2 marching cubes
> runs that have been appended. Now I understand why you asked if
> MarchingCubes streamed? This is what you would expect if you ran it
> twice and appended the results.
>
> Try removing both the
> cubes->Update();
> and
> cubes->UpdateWholeExtent();
>
> On Wed, Jul 29, 2009 at 9:13 AM, Dominik Szczerba<dominik at itis.ethz.ch> wrote:
>> The files are here:
>>
>> http://otoro.itis.ethz.ch/~dominik/tmp/test_smooth.vti
>> http://otoro.itis.ethz.ch/~dominik/tmp/test_cubes.vtk
>>
>> The pipeline is:
>>
>> // setup (in a constructor)
>> extractVOI = vtkSmartPointer<vtkExtractVOI>::New();
>> extractVOI->SetInput(viewer->image);
>>
>> calculator = vtkSmartPointer<vtkArrayCalculator>::New();
>> calculator->SetInputConnection(extractVOI->GetOutputPort());
>> calculator->SetResultArrayType(VTK_FLOAT);
>>
>> ismooth = vtkSmartPointer<vtkImageGaussianSmooth>::New();
>> ismooth->SetInputConnection(calculator->GetOutputPort());
>> ismooth->BreakOnError();
>> ismooth->SetDimensionality(3);
>>
>> cubes = vtkSmartPointer<vtkMarchingCubes>::New();
>> cubes->SetInputConnection(ismooth->GetOutputPort());
>> cubes->SetNumberOfContours(1);
>> cubes->SetComputeNormals(0);
>> cubes->SetComputeGradients(0);
>> cubes->SetComputeScalars(0);
>>
>> // all below is (being continuously) called from a separate function
>> // FIXME why is this required???
>> vtkSmartPointer<vtkStructuredPoints> image2 =
>> (vtkStructuredPoints*)calculator->GetOutput();
>> image2->SetScalarTypeToFloat();
>>
>> ismooth->SetInput(image2);
>> ismooth->SetRadiusFactors(radius,radius,radius);
>> ismooth->SetStandardDeviations(sigma,sigma,sigma);
>>
>> vtkNew(vtkXMLImageDataWriter,writer);
>> writer->SetInput(ismooth->GetOutput());
>> writer->SetFileName("test_smooth.vti");
>> writer->Write();
>>
>> cubes->Update();
>> cubes->UpdateWholeExtent();
>>
>> vtkNew(vtkPolyDataWriter,poly_writer);
>> poly_writer->SetInput(cubes->GetOutput());
>> poly_writer->SetFileName("test_cubes.vtk");
>> poly_writer->SetFileTypeToBinary();
>> poly_writer->Write();
>>
>>
>> There is a small dirty part that I do not like (FIXME, otherwise the output
>> type is somehow unsigned char) but otherwise it is rather simple and clean.
>>
>> Looking forward some ideas about the origin of the degenerate points - and
>> once again, only on one system and not the other.
>>
>> With regards,
>> Dominik
>>
>> Bill Lorensen wrote:
>>> MarchingCubes does not stream. Also, internally it uses vtkMergePoints
>>> to make sure that duplicate points are removed. I don't see how memory
>>> size should affect the results.
>>>
>>> What version of VTK are you using?
>>>
>>> Also, can you put the data online somewhere?
>>>
>>> Bill
>>>
>>> On Wed, Jul 29, 2009 at 3:27 AM, Dominik Szczerba<dominik at itis.ethz.ch>
>>> wrote:
>>>> I am doing nothing particular, just a structured points dataset with a
>>>> smooth scalar field (float) that I am running vtkMarchingCubes on. I get
>>>> my
>>>> polydata as cubes->GetOutput(). As mentioned, I dont know if that matters
>>>> but the problem appears on a low mem PC and not on a bigger one (same
>>>> code
>>>> but different systems). If you strongly believe there is something
>>>> special
>>>> in my image data I can put it online for a test.
>>>>
>>>> I can not follow the vtkMarchingCubes code well enough to clearly tell if
>>>> there is some streaming being done - looks to me like not, but where do
>>>> the
>>>> degenerate points come from?
>>>>
>>>> An interesting observation though, if I save the resulting polydata using
>>>> vtkPolyDataWriter I get the file you saw. If I save it with the vtkSTL
>>>> writer I get a clean dataset, so the latter must merge coincident points
>>>> internally (why? - this removes the chance of finding errors)
>>>>
>>>> best regards,
>>>> Dominik
>>>>
>>>> Bill Lorensen wrote:
>>>>> I looked at the vtk file and indeed it has multiple surfaces. How did
>>>>> you generate this polydata? Can you tell me the pipeline you used?
>>>>>
>>>>> On Sun, Jul 26, 2009 at 1:29 PM, Dominik Szczerba<dominik at itis.ethz.ch>
>>>>> wrote:
>>>>>> On Sun, 2009-07-26 at 12:35 -0400, Bill Lorensen wrote:
>>>>>>> I am surprised at this. vtkMarchingCubes should produce manifold and
>>>>>>> oriented surfaces. There should be no duplicate points.
>>>>>>> vtkMarchingCubes can produce multiple, topologically disconnected
>>>>>>> surfaces. vtkDiscreteMarchingCubes can (and should) produce
>>>>>>> geometrically continuous but topologically disconnected surafces.
>>>>>>>
>>>>>>> Can you provide a test dataset that reproduces the problem?
>>>>>>>
>>>>>> I hanged a small sample on:
>>>>>>
>>>>>> http://otoro.itis.ethz.ch/~dominik/tmp/test.vtk
>>>>>>
>>>>>> I got this while segmenting a smooth scalar field on a (Windows
>>>>>> virtual)
>>>>>> machine with very little memory. I do not get this on a (linux real)
>>>>>> machine with lots of memory.
>>>>>>
>>>>>> Running connectivity filter you will notice a few disconnected regions.
>>>>>> It goes away after merging coincident points (and the number of points
>>>>>> is reduced indicating degenerate original points).
>>>>>>
>>>>>> I just need to get a warning when the output is in such condition to
>>>>>> not
>>>>>> have to merge points by default, which degrades performance.
>>>>>>
>>>>>> -- Dominik
>>>>>>
>>>>>>> Bill
>>>>>>>
>>>>>>> On Sun, Jul 26, 2009 at 8:27 AM, Dominik
>>>>>>> Szczerba<dominik at itis.ethz.ch>
>>>>>>> wrote:
>>>>>>>> I have experimentally found out that vtkMarchingCubes can generate
>>>>>>>> geometrically continuous but topologically disconnected isosurfaces,
>>>>>>>> i.e. the isosurface is cut into stripes along one axis with duplicate
>>>>>>>> points on the edges. How do I get a control of this behavior,
>>>>>>>> especially, to know if there will be disconnected stripes so I should
>>>>>>>> merge the points (I need topological consistency)?
>>>>>>>>
>>>>>>>> -- Dominik
>>>>>>>>
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>>
>> --
>> d o m i n i k s z c z e r b a , p h d . . . . . . . . . . .
>> c o m p u t a t i o n a l l i f e s c i e n c e g r o u p
>> . . . . . . . i t ' i s r e s e a r c h f o u n d a t i o n
>> . . . . . . . . . . . . . . . . . . . . http://www.itis.ethz.ch
>>
>>
>
--
d o m i n i k s z c z e r b a , p h d . . . . . . . . . . .
c o m p u t a t i o n a l l i f e s c i e n c e g r o u p
. . . . . . . i t ' i s r e s e a r c h f o u n d a t i o n
. . . . . . . . . . . . . . . . . . . . http://www.itis.ethz.ch
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