[vtkusers] avoiding/removing non-manifold parts from the result of vtkMarchingCubes
Dr. Roman Grothausmann
grothausmann.roman at mh-hannover.de
Fri Aug 2 16:59:06 EDT 2013
On 02/08/13 22:50, Bill Lorensen wrote:
>
> 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.
I will. Many thanks for the solution.
What should I read to understand that a non-integral value circumvents the
problem (and that an integral value causes it)?
Also I've searched long for an explanation what causes the difference concerning
surface smoothness using vtkMarchingCubes on a binary image or one that has a
gradient (understanding that that allows to calculate normals pointing in more
than 26 directions) simply created with a mean-filer on the binary image. Is
there a kind of additional internal filter that only is applied if the input has
gradients?
Many thanks Bill for looking into this.
Roman
> On Fri, Aug 2, 2013 at 4:30 PM, Bill Lorensen <bill.lorensen at gmail.com
> <mailto: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
> <mailto: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
> <mailto:grothausmann.roman at mh-hannover.de>
> <mailto:grothausmann.roman at mh-__hannover.de
> <mailto: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
> <mailto:grothausmann.roman at mh-__hannover.de>
> <mailto:grothausmann.roman at mh-__hannover.de
> <mailto:grothausmann.roman at mh-hannover.de>>
> <mailto:grothausmann.roman at mh-____hannover.de
> <mailto:grothausmann.roman at mh-__hannover.de>
>
> <mailto:grothausmann.roman at mh-__hannover.de
> <mailto: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>
> <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 <tel:%2B49%20511%20532-9574>
>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
>
>
>
> --
> 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
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