[vtkusers] streaming vtkMarchingCubes?

Dominik Szczerba dominik at itis.ethz.ch
Wed Jul 29 09:13:25 EDT 2009 

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
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>
>> --
>> 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

More information about the vtkusers mailing list