[vtkusers] avoiding/removing non-manifold parts from the result of vtkMarchingCubes
Bill Lorensen
bill.lorensen at gmail.com
Mon Aug 5 07:27:34 EDT 2013
It does not look like 0/255 segmented data. I'll take a look leter today.
On Mon, Aug 5, 2013 at 1:44 AM, Dr. Roman Grothausmann <
grothausmann.roman at mh-hannover.de> wrote:
> On 02/08/13 23:14, Bill Lorensen wrote:
>
>> vtkDiscreteMarchingCubes should be used for segmented data.
>> vtkMarchingCubes for
>> "continuous" data.
>>
>> In your case, a medical dataset, it is unusual to have 8 bit data. Most
>> medical
>> data (e.g. DICOM) is 16 bit.
>>
>
> Well, it is preprocessed med. data. Originally it is 16bit but we have to
> segment it semi-manually with itksnap, so we end up with a binary image
> (either 0 or 255). As we have a certain uncertainty in the borders of the
> segmentation and some segmentation border voxels with e.g. 2 adjacent bg
> voxels, a mean or gauss filter is applied which yields the "continous"
> data. Applying vtkMarchingCubes at level 127 gives a surface much smoother
> than using either itkAntiAliasBinaryImageFilter or vtkWindowedSincFilter
> afterwards.
>
> Still, I wonder what causes the smoothness of vtkMarchingCubes surface. If
> I understand it correctly, vtkDiscreteMarchingCubes (despite its 256
> mc-cases) only creates triangles whose normals can point in only 26
> discrete orientations. vtkMarchingCubes on a binary image (containing only
> values of 0 or 255) seems to generate the same surface using a level of
> 127. Now if I have "continuous" data, vtkMarchingCubes seems to generate
> triangles oriented in far more than 26 discrete directions. Are the
> triangle orientations of the 256 mc-cases adjusted to point in the
> direction of the image-gradient in a second step of vtkMarchingCubes? Are
> the cube-contour intersection positions of the 256 mc-cases adjusted as
> well, i.e. not restricted any more to intersect the cube edges in the
> middle of the edge?
>
>
>
>>
>> On Fri, Aug 2, 2013 at 4:59 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 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 <bill.lorensen at gmail.com>>
>> <mailto:bill.lorensen at gmail.__**com <mailto:bill.lorensen at gmail.*
>> *com <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<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:
>>
>> 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>
>> >
>> <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>
>> <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:
>>
>> 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>
>> >>
>> <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>
>> <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>
>> >
>>
>> <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>
>> <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>
>> <tel:%2B49%20511%20532-9574>
>> <tel:%2B49%20511%20532-9574>
>>
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>> >>>
>>
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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>
>> <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 <tel:%2B49%20511%20532-9574>
>>
>>
>>
>>
>> --
>> 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
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