[vtkusers] avoiding/removing non-manifold parts from the result of vtkMarchingCubes
Bill Lorensen
bill.lorensen at gmail.com
Fri Aug 2 16:50:28 EDT 2013
Since your data is unsigned char, and you used an isovalue of 127, I
suspect there must be some degenerate triangles produced. I did produce two
nonmanifold edges with isovalue 127 (I'm surprised).
Try specifying a non-integral value (e.g. 127.001). I do not see
non-manifold edges with that value.
On Fri, Aug 2, 2013 at 4:30 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
> Great. I generated a surface. It will take be a few minutes to generate
> feature edges.
>
>
>
> On Fri, Aug 2, 2013 at 4:25 PM, Dr. Roman Grothausmann <
> grothausmann.roman at mh-hannover.de> wrote:
>
>> On 02/08/13 22:20, Bill Lorensen wrote:
>>
>>> what level do you use?
>>>
>>
>> Sorry, forgot to mention that: level 127
>>
>>
>>>
>>>
>>> On Fri, Aug 2, 2013 at 4:07 PM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-**hannover.de <grothausmann.roman at mh-hannover.de><mailto:
>>> grothausmann.roman at mh-**hannover.de <grothausmann.roman at mh-hannover.de>
>>> >>
>>>
>>> wrote:
>>>
>>> On 02/08/13 16:06, Bill Lorensen wrote:
>>>
>>> Marching Cubes should not generate non-manifold surfaces. The
>>> offending
>>> triangle
>>> looks suspicious. What does the rest of your pipeline look like?
>>>
>>>
>>> Thanks Bill for looking into this. I get the very same output using
>>> paraview
>>> and its contour filter when ticking "Generate Triangles" or using
>>> vmtkmarchingcubes (which seems to use only vtkMarchingCubes in
>>> vmtkmarchingcubes.py). To check it trice I used the simple program
>>> below and
>>> got the same output again. Only paraview and its contour filter
>>> without
>>> ticking "Generate Triangles" yields a different result.
>>>
>>> _____________________________
>>>
>>> #include <vtkSmartPointer.h>
>>> #include <vtkMetaImageReader.h>
>>> //#include <vtkImageConstantPad.h>
>>> #include <vtkMarchingCubes.h>
>>> #include <vtkXMLPolyDataWriter.h>//for vtp-files
>>>
>>> #include <vtkCallbackCommand.h>
>>> #include <vtkCommand.h>
>>>
>>>
>>> void ProgressFunction ( vtkObject* caller, long unsigned int
>>> eventId, void*
>>> clientData, void* callData )
>>> {
>>>
>>> vtkAlgorithm *d= static_cast<vtkAlgorithm*>(__**caller);
>>>
>>> fprintf(stderr, "\rFilter progress: %5.1f%%", 100.0 *
>>> d->GetProgress());
>>> std::cerr.flush();
>>>
>>> }
>>>
>>> int main(int argc, char* argv[]){
>>> if( argc != 5 )
>>> {
>>> std::cerr << "Usage: " << argv[0];
>>> std::cerr << " inputImage";
>>> std::cerr << " outputMesh";
>>> std::cerr << " level normals";
>>> std::cerr << std::endl;
>>> return EXIT_FAILURE;
>>> }
>>>
>>> if(!(strcasestr(argv[1],".mhd"**__))) {
>>>
>>> std::cout << "The input should end with .mhd" << std::endl;
>>> return -1;
>>> }
>>>
>>> if(!(strcasestr(argv[2],".vtp"**__))) {
>>>
>>> std::cout << "The input should end with .vtp" << std::endl;
>>> return -1;
>>> }
>>>
>>> vtkSmartPointer<__**vtkCallbackCommand> progressCallback =
>>> vtkSmartPointer<__**vtkCallbackCommand>::New();
>>> progressCallback->SetCallback(**__ProgressFunction);
>>>
>>> vtkSmartPointer<__**vtkMetaImageReader> reader =
>>> vtkSmartPointer<__**vtkMetaImageReader>::New();
>>>
>>>
>>> reader->SetFileName(argv[1]);
>>> reader->Update();
>>>
>>> vtkSmartPointer<__**vtkMarchingCubes> mc=
>>> vtkSmartPointer<__**vtkMarchingCubes>::New();
>>>
>>> mc->SetInputConnection(reader-**__>GetOutputPort());
>>>
>>> mc->SetValue(0, atof(argv[3]));
>>> //mc->ComputeNormalsOn();
>>> mc->SetComputeNormals(atoi(__**argv[4]));
>>>
>>> //mc->ComputeGradientsOn();
>>> //mc->ComputeScalarsOn();
>>> std::cout << "Executing discrete marching cubes..." <<
>>> std::endl;
>>> mc->AddObserver(vtkCommand::__**ProgressEvent,
>>> progressCallback);
>>>
>>> mc->Update();
>>> std::cout << std::endl << "done." << std::endl;
>>>
>>> vtkSmartPointer<__**vtkXMLPolyDataWriter> Pwriter =
>>> vtkSmartPointer<__**vtkXMLPolyDataWriter>::New();
>>> Pwriter->SetFileName(argv[2]);
>>> Pwriter->SetInputConnection(__**mc->GetOutputPort());
>>>
>>>
>>> Pwriter->Update();
>>>
>>> return EXIT_SUCCESS;
>>> }
>>>
>>>
>>>
>>>
>>>
>>> On Fri, Aug 2, 2013 at 8:23 AM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-__**hannover.de<grothausmann.roman at mh-__hannover.de>
>>> <mailto:grothausmann.roman at mh-**hannover.de<grothausmann.roman at mh-hannover.de>
>>> >
>>> <mailto:grothausmann.roman at mh-**__hannover.de<grothausmann.roman at mh-__hannover.de>
>>>
>>> <mailto:grothausmann.roman at mh-**hannover.de<grothausmann.roman at mh-hannover.de>
>>> >>>
>>>
>>> wrote:
>>>
>>> Dear mailing list members,
>>>
>>>
>>> Recently, I came across a voxel-dataset that when meshed
>>> with
>>> vtkMarchingCubes results in a mesh that contains
>>> non-manifold edges
>>> (magenta
>>> line in attached image).
>>> How can this be avoided?
>>> Using paraview's contour filter and switching off "Generate
>>> Triangles"
>>> creates a slightly different surface mesh that does not
>>> contain
>>> non-manifold
>>> edges. However vtkMarchingCubes does not seem to have any
>>> option
>>> concerning
>>> triangulation.
>>> What filter/option do I have to use to get the same result
>>> just
>>> with pure VTK?
>>>
>>> As a workaround: Is it possible to split the mesh at
>>> non-manifold
>>> edges?
>>> vtkIntersectionPolyDataFilter sounds promising but seems to
>>> need
>>> surfaces
>>> not just the edges.
>>>
>>> Any help or hints are very much appreciated
>>> Roman
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>>>
>>>
>>> --
>>> Dr. Roman Grothausmann
>>>
>>> Tomographie und Digitale Bildverarbeitung
>>> Tomography and Digital Image Analysis
>>>
>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>> Medizinische Hochschule Hannover
>>> Carl-Neuberg-Str. 1
>>> D-30625 Hannover
>>>
>>> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
>>>
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>>> >
>>>
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
--
Unpaid intern in BillsBasement at noware dot com
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