[vtkusers] Rendering/Computing normals of a surface

Thu Apr 18 06:04:05 EDT 2013

Hi Bill,

that worked out well. Now my normals have the correct color.

I am still struggling how I could visualize a Subset of normals of my surface. I can select the normal subset like this:

    vtkSmartPointer<vtkFloatArray> normals = vtkSmartPointer<vtkFloatArray>::New();
    normals->SetNumberOfComponents(3);
     vtkSmartPointer<vtkIdList> IDs = //a containing about 200 IDs of all normals I would like to see
      for(int j = 0; j < IDs->GetNumberOfIds(); ++j)
      {
          normals->InsertNextTuple( normalGenerator->GetOutput()->GetPointData()->GetNormals()->GetTuple(IDs->GetId(j)) );
      }

However, if I set these normals for my polydata and try to render everything a crash occurs inside the Update() of the glyph3d. I assume that the glyph3d is struggling, because I insert a polydata with 300k points and add only 200 normals.

I could also select the corresponding 200 points from the polydata and make a new polydata containing 200 points and 200 normals. Is this the "optimal" way to go?

Regards
Thomas

From: Bill Lorensen [mailto:bill.lorensen at gmail.com]
Sent: Montag, 15. April 2013 18:47
To: Kilgus, Thomas
Cc: vtkusers at vtk.org
Subject: Re: [vtkusers] Rendering/Computing normals of a surface

Have you set the ScalarRange on the Mapper? You should set it to the range of your scalar data. If you do not want to display scalar colors, apply SetScalarVisibilityOff() to your mapper.

On Mon, Apr 15, 2013 at 11:51 AM, Kilgus, Thomas <t.kilgus at dkfz-heidelberg.de<mailto:t.kilgus at dkfz-heidelberg.de>> wrote:
Hey Bill,

I just figured out that the normals of my Kinect data are indeed there. They are just rendered very small and in dark blue on a black renderwindow. I set the color of the actor to red and don't use the SetColorMode method of the glyph3d (I tried to use it, but it didn't change anything). The normals of my ball are rendered in red. Do you have any idea why my Kinect data has blue glyphs and ignores all color calls? Does this "blue" have any meaning?

Regards,
Thomas

From: Bill Lorensen [mailto:bill.lorensen at gmail.com<mailto:bill.lorensen at gmail.com>]
Sent: Freitag, 12. April 2013 16:44

To: Kilgus, Thomas
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Subject: Re: [vtkusers] Rendering/Computing normals of a surface

The mapping is 1:1. There will be a normal for each point and a normal for each cell.

On Fri, Apr 12, 2013 at 10:30 AM, Kilgus, Thomas <t.kilgus at dkfz-heidelberg.de<mailto:t.kilgus at dkfz-heidelberg.de>> wrote:
Sorry, either this example is not the answer to my question or I don't get it :).

I have N normals inside a vtkDoubleArray and V vertices inside a vtkPolyData. How can I get the corresponding normal(s) N(j) to vertex V(i). I think i != j, because when splitting is on NumberOfNormals != NumberOfVertices, or not? In other words, the mapping is NOT 1:1.

The example simply adds 3 normals to 3 points and here the mapping is 1:1.

From: Bill Lorensen [mailto:bill.lorensen at gmail.com<mailto:bill.lorensen at gmail.com>]
Sent: Freitag, 12. April 2013 16:21

To: Kilgus, Thomas
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Subject: Re: [vtkusers] Rendering/Computing normals of a surface

Look at this example:
http://vtk.org/Wiki/VTK/Examples/Cxx/PolyData/PolyDataPointNormals

On Fri, Apr 12, 2013 at 9:04 AM, Kilgus, Thomas <t.kilgus at dkfz-heidelberg.de<mailto:t.kilgus at dkfz-heidelberg.de>> wrote:
And how would I get the normal of a certain vertex? Especially with SplittingOn()

From: Bill Lorensen [mailto:bill.lorensen at gmail.com<mailto:bill.lorensen at gmail.com>]
Sent: Freitag, 12. April 2013 14:57

To: Kilgus, Thomas
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Subject: Re: [vtkusers] Rendering/Computing normals of a surface

2) vtkPlaneSource generates normals. Many of the source's do.

After
 normalGenerator->Update();
try
normalGenerator->GetOutput()->Print(std::cout);
to see if there are normals present

On Fri, Apr 12, 2013 at 8:45 AM, Kilgus, Thomas <t.kilgus at dkfz-heidelberg.de<mailto:t.kilgus at dkfz-heidelberg.de>> wrote:
Unfortunately, that is a bit complicated and inside our own framework. But basically, this happens:

vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
points->SetDataTypeToDouble();
vtkSmartPointer<vtkCellArray> polys = vtkSmartPointer<vtkCellArray>::New();

for loop for all pixels of the depth image
{
Insert 3d point into points

Insert cell points for valid (!=0) points with valid neighbors (simple triangulation)
}

vtkSmartPointer<vtkPolyData> mesh = vtkSmartPointer<vtkPolyData>::New();
mesh->SetPoints(points);
mesh->SetPolys(polys);

We also add texture coordinates and scalars, but this is not related to normals, is it?

You can see the details here: http://mitk.org/git/?p=MITK.git;a=blob;f=Modules/ToFProcessing/mitkToFDistanceImageToSurfaceFilter.cpp;h=2b24b193315c2db97bce1d4f8aed90df42c99d1f;hb=HEAD

My questions 3. and 4.  are not related to the Kinect data, are they?

Regards,
Thomas

From: Bill Lorensen [mailto:bill.lorensen at gmail.com<mailto:bill.lorensen at gmail.com>]
Sent: Freitag, 12. April 2013 14:36
To: Kilgus, Thomas
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Subject: Re: [vtkusers] Rendering/Computing normals of a surface

How are you creating your Kinect mesh?

On Fri, Apr 12, 2013 at 8:28 AM, Kilgus, Thomas <t.kilgus at dkfz-heidelberg.de<mailto:t.kilgus at dkfz-heidelberg.de>> wrote:
Hi everyone,

I'm trying to compute and render normals of certain vertices of a mesh (in fact a Kinect mesh). I assume that I have to compute the normals via vtkPolyDataNormals and display them using a vtkGlyph3d?

I observed some strange behavior which really confused me:

1.       If I create a vtkPlaneSource or load a ball from hard disc and compute normals for that data, everything seems fine. If I load an "open" surface (my Kinect mesh), there are no normals displayed. The documentation says that SetAutoOrientNormals does only work with closed surfaces. But at the moment I don't care about orientation. There should be normals for at least some vertices of an open mesh, shouldn't there?

2.       If I load my Kinect mesh and make a new polydata which contains as much points at (0,0,0) as I have normals and set the normals for the new polydata, the glyph will produce arrows pointing from (0,0,0) to somewhere. This looks pretty good could but could be a random result with empty memory.

3.       If I connect my vtkPlaneSource or the ball directly to the glyph (I skip the vtkPolyDataNormals), normals are still rendered correctly. Does this mean my vtkPlaneSource already contains them from the beginning? Are they computed in the background somewhere inside the glyph3d? Is the vtkPolyDataNormals even necessary? This only works for the plane and the ball - not for the Kinect mesh. I can imagine that a plane automatically computes its normal on Update(), but why does my ball have normals already?

4.       How can I get the normal of a certain vertex Id? If I use vtkFloatArray::SafeDownCast(output->GetPointData()->GetNormals()) are Id's equal to the vertex Id's of the polydata? What happens if I turn splitting on and get multiple normals for each vertex? How is the mapping done?

My code looks as follows:

vtkSmartPointer<vtkPolyData> inputPolyData = //load some data

  // Generate normals
  vtkSmartPointer<vtkPolyDataNormals> normalGenerator = vtkSmartPointer<vtkPolyDataNormals>::New();
  normalGenerator->SetInput( inputPolyData );
  normalGenerator->ComputePointNormalsOn();
  normalGenerator->ComputeCellNormalsOff();
  normalGenerator->SetSplitting(0); //I want exactly one normal per vertex
  normalGenerator->Update();

  vtkSmartPointer<vtkPolyDataMapper> mapperNormals =
      vtkSmartPointer<vtkPolyDataMapper>::New();

  //I chose arrows as representation
  vtkSmartPointer<vtkArrowSource> arrow = vtkSmartPointer<vtkArrowSource>::New();
  arrow->Update();

//use the output of vtkPolyDataNormals as input for the glyph3d
vtkSmartPointer<vtkGlyph3D> glyph = vtkSmartPointer<vtkMaskedGlyph3D>::New();
  glyph->SetInput( normalGenerator->GetOutput() );
  glyph->SetSourceConnection(arrow->GetOutputPort());
  glyph->OrientOn();
  glyph->SetVectorModeToUseNormal();
  glyph->Update();

  mapperNormals->SetInputConnection(glyph->GetOutputPort());

//now follows standard code which could be taken from almost any example...
  vtkSmartPointer<vtkActor> actorNormals =
      vtkSmartPointer<vtkActor>::New();
  actorNormals->SetMapper(mapperNormals);

  // Create a renderer, render window, and interactor
  vtkSmartPointer<vtkRenderer> renderer =
      vtkSmartPointer<vtkRenderer>::New();
  vtkSmartPointer<vtkRenderWindow> renderWindow =
      vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->AddRenderer(renderer);
  vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
      vtkSmartPointer<vtkRenderWindowInteractor>::New();
  vtkSmartPointer<vtkInteractorStyleTrackballCamera> style = vtkSmartPointer<vtkInteractorStyleTrackballCamera>::New();
  renderWindowInteractor->SetInteractorStyle(style);
  renderWindowInteractor->SetRenderWindow(renderWindow);

  // Add the actor to the scene
  renderer->AddActor(actorNormals);

  // Render and interact
  renderWindow->Render();
  renderWindowInteractor->Start();

Regards,
Thomas

Thomas Kilgus
German Cancer Research Center (DKFZ)
Div. Medical and Biological Informatics
Junior group: Computer-assisted Interventions (E131)
Im Neuenheimer Feld 280
69120 Heidelberg, Germany
Phone: +49(0) 6221-42-3545<tel:%2B49%280%29%206221-42-3545>

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