[vtkusers] Creating a contour from volume data

[Rene Tschirley]

Dear VTK gurus,


I'm quite near to despairation. With upgrading to VTK 4.0 (I used to work
with 2.3 and 3.2 by now) I rearranged some applications. But now, I seem
to be unable to create a simple isosurface from a volume dataset as it
worked quite well with 2.3 and 3.2. It's a pity that there are so few
examples for 4.0, especially the most interesting examples have been
removed, e.g. medical[1-3].cxx, so I have nothing to look at how things
work well.

Here's the relevant C++ code:

  vtkImageReader *reader = vtkImageReader::New();
  reader->SetFilePrefix(filename);
  reader->SetFileNameSliceOffset(sliceoffset);
  reader->SetFilePattern(pattern);
  reader->SetDataExtent(0, xsize-1, 0, ysize-1, 0, zsize-1);
  reader->SetDataScalarTypeToUnsignedChar();
  reader->SetDataSpacing (xspacing, yspacing, zspacing);
  reader->SetDataMask(mask);
  reader->Update();
  cout << "Reader has " 
       << reader->GetOutput()->GetNumberOfPoints() 
       << "points.\n"; // at runtime this tells me that there are
                       // 13107200 data cells available which is
                       // correct for 512*512*50 @ 8bpp

  vtkImageShrink3D *shrinker = vtkImageShrink3D::New();
  shrinker->SetShrinkFactors(xshrink,yshrink,zshrink);
  shrinker->SetInput(reader->GetOutput());
  shrinker->Update();  // a PrintSelf() makes me sure that I didn't loose
                       // any points yet.

  vtkMarchingCubes *skinExtractor = vtkMarchingCubes::New();
  skinExtractor->SetInput(shrinker->GetOutput());
  skinExtractor->SetValue(0, isolevel);
  cout << "Creating " << skinExtractor->GetOutput()->GetNumberOfPolys()
       << " polygons.\n";
                       // at runtime this tells me that there are
                       // 0 polygons created which is obviously not what
                       // I wanted.

After that I use vtkDecimatePro and vtkPolyDataMapper to continue the
pipeline, but without any polygons, the pipeline is not of any use.

Below follows the PrintSelf() output of reader->GetOutput() and Marching
Cubes object if this is of any help.

This part of the pipeline worked well with VTK 2.3 and 3.2 so I wonder if
there is any little nifty mistake in it. I hope somebody of you will
point it out.


Yours,
	René


PrintSelf of reader->GetOutput:
Debug: Off
Modified Time: 128
Reference Count: 1
Registered Events: (none)
Source: 0x8055328
Release Data: Off
Data Released: False
Global Release Data: Off
MaximumNumberOfPieces: -1
PipelineMTime: 122
UpdateTime: 129
UpdateExtent: Not Initialized
Update Number Of Pieces: 1
Update Piece: 0
Update Ghost Level: 0
RequestExactExtent: Off
 UpdateExtent: 0, 511, 0, 511, 0, 49
WholeExtent: 0, 511, 0, 511, 0, 49
Field Data:
  Debug: Off
  Modified Time: 71
  Reference Count: 1
  Registered Events: (none)
  Number Of Arrays: 0
  Number Of Components: 0
  Number Of Tuples: 0
Locality: 0
NumberOfConsumers: 0
ExtentTranslator: (0x8055680)
MaximumNumberOfPieces: -1
Number Of Points: 13107200
Number Of Cells: 12794929
Cell Data:
  Debug: Off
  Modified Time: 75
  Reference Count: 1
  Registered Events: (none)
  Number Of Arrays: 0
  Number Of Components: 0
  Number Of Tuples: 0
  Copy Flags: ( 1 1 1 1 1 )
  Scalars: (none)
  Vectors: (none)
  Normals: (none)
  TCoords: (none)
  Tensors: (none)
Point Data:
  Debug: Off
  Modified Time: 128
  Reference Count: 1
  Registered Events: (none)
  Number Of Arrays: 1
  Array 0 name = ImageValues
  Number Of Components: 1
  Number Of Tuples: 13107200
  Copy Flags: ( 1 1 1 1 1 )
  Scalars: 
    Debug: Off
    Modified Time: 125
    Reference Count: 1
    Registered Events: (none)
    Name: ImageValues
    Number Of Components: 1
    Number Of Tuples: 13107200
    Size: 13107200
    MaxId: 13107199
    LookupTable: (none)
    Array: 0x4254a008
  Vectors: (none)
  Normals: (none)
  TCoords: (none)
  Tensors: (none)
Bounds: 
  Xmin,Xmax: (0, 511)
  Ymin,Ymax: (0, 511)
  Zmin,Zmax: (0, 49)
Compute Time: 0
Release Data: Off
ScalarType: 3
NumberOfScalarComponents: 1
Spacing: (1, 1, 1)
Origin: (0, 0, 0)
Dimensions: (512, 512, 50)
Increments: (1, 512, 262144)
Extent: (0, 511, 0, 511, 0, 49)
WholeExtent: (0, 511, 0, 511, 0, 49)

PrintSelf of skinExtractor (vtkMarchingCubes):
number of contours = 1
Debug: Off
Modified Time: 153
Reference Count: 2
Registered Events: (none)
Number Of Required Inputs: 1
Input 0: (0x80553c0)
AbortExecute: Off
Progress: 1
Progress Text: (None)
Output 0: (0x8058a98)
Contour Values: 
  Value 0: 30
Compute Normals: On
Compute Gradients: Off
Compute Scalars: On
Locator:0x8059060
  Debug: Off
  Modified Time: 153
  Reference Count: 1
  Registered Events: (none)
  DataSet: (none)
  Automatic: On
  Tolerance: 0.001
  Level: 8
  MaxLevel: 8
  Retain Cell Lists: On
  Build Time: 0
  Number of Points Per Bucket: 3
  Divisions: (42, 42, 42)

-- 
Dipl.-Inform. René Tschirley              http://www.cs.tu-berlin.de/~pooh
TU Berlin, Computer Graphics and Computer Assisted Medicine research group
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