[vtkusers] streaming vtkMarchingCubes?
Dominik Szczerba
dominik at itis.ethz.ch
Wed Jul 29 16:38:30 EDT 2009
I excluded those lines, but the problem persists. The output dataset is
here:
http://otoro.itis.ethz.ch/~dominik/tmp/test_cubes2.vtk
It may be non-obvious to notice it though, as there are hundreds of
disconnected pixels. You need to set the color scale to e.g. 0:3 to see
the large two disconnected bulks.
I have also run vtkMarchingCubes with DebugOn. The log is here:
http://otoro.itis.ethz.ch/~dominik/tmp/log
What I make of it is that due to the little available memory the filter
executes in stripes and/or does not use vtkMergePoints. If so, I thing
the user must have a way to get himself informed to call MergePoints
himself. Otherwise it might be a rare bug with MergePoints that I would
like to fix.
with regards,
Dominik
Bill Lorensen wrote:
> Also, try removing all of these:
> // 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();
>
> On Wed, Jul 29, 2009 at 12:23 PM, Bill Lorensen<bill.lorensen at gmail.com> wrote:
>> 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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>>>>>>>
>>>>>>>
>>>>> --
>>>>> 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
>>>
>>>
>
--
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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