[vtkusers] streaming vtkMarchingCubes?
Bill Lorensen
bill.lorensen at gmail.com
Wed Jul 29 12:23:06 EDT 2009
I can't explain it.
BTW, what contour value do you set.
On Wed, Jul 29, 2009 at 12:06 PM, Dominik Szczerba<dominik at itis.ethz.ch> wrote:
> 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 . . . . . . . . . . .
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>>>>> . . . . . . . . . . . . . . . . . . . . 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
>>>
>>>
>>
>
>
> --
> 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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