[Insight-users] Problem of writing .png to .vtk volume

[Luis Ibanez]

Hi Yili,


1) You are using unsigned char as the pixels type.

2) Does that mean that the .png images were the
    result of rescaling an input CT(?) volume down
    to 8 bits ?

3) Most likely you iso-contour value of 128.0 is
     not the proper value for extracting the lung,
    given the intensity scale that you have now.


4) If you were using CT (in Hounsfield units)
    you probably should use a threshold value
    close to 700HU.

5) Also, given that the lungs are an internal structure,
    you will need to do a segmentation in order to get
    something clear to visualize. Otherwise, what you
    are going to get as a surface now is a combination
    of the external surfaces (skin) and internal surfaces
    (lung wall and lung vasculature).


6) What you may want to do first is to load your image
     series in to Paraview (www.paraview.org) and to
     experiment with it Contour filter at different threshold
     values. This will give you an idea of the correct value
     to use.


  Regards,


        Luis



--------------------------------------------------------------------------------------
On Thu, Sep 10, 2009 at 11:11 AM, Yili Pan <pyl0420 at gmail.com> wrote:
> Hi everyone:
>
> I have a series of .png lung data and I use ImageSeriesReadWrite example to
> write the series into volume. Then I use VTK to display the volume.
> The former part of the project seems to work well, since I got the .vtk
> volume. However, the window shows nothing at last when I was trying to use
> vtkContourFilter as the filter to display the lung.
> I am not sure if I missed to set some data of the volume or this is the
> visualization problem. Can you help me with this?
> Thanks a lot!
> Best,
> Yili
> This is the code I changed from the example:
> int main( int argc, char ** argv )
> {
>
>   if( argc < 4 )
>     {
>     std::cerr << "Usage: " << std::endl;
>     std::cerr << argv[0] << " firstSliceValue lastSliceValue
>  outputImageFile " << std::endl;
>     return EXIT_FAILURE;
>     }
>
>
>   typedef unsigned char                       PixelType;
>   const unsigned int Dimension = 3;
>   typedef itk::Image< PixelType, Dimension >  ImageType;
>   typedef itk::ImageSeriesReader< ImageType >  ReaderType;
>   typedef itk::ImageFileWriter<   ImageType >  WriterType;
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>   const unsigned int first = atoi( argv[1] );
>   const unsigned int last  = atoi( argv[2] );
>   const char * outputFilename = argv[3];
> //============================================Reader
> Part==============================================
>   typedef itk::NumericSeriesFileNames    NameGeneratorType;
>   NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>
>
>   nameGenerator->SetSeriesFormat( "h1-1.%03d.png" );
>   nameGenerator->SetStartIndex( first );
>   nameGenerator->SetEndIndex( last );
>   nameGenerator->SetIncrementIndex( 1 );
>   system("pause");
>   itk::PNGImageIO::Pointer pngIO=itk::PNGImageIO::New();
>   pngIO->SetNumberOfDimensions(3);
>
>   pngIO->SetDimensions(0,512);
>   pngIO->SetDimensions(1,512);
>   pngIO->SetDimensions(2,259);
>   reader->SetImageIO( pngIO);
>
>
>
>   reader->SetFileNames( nameGenerator->GetFileNames()  );
>   system("pause");
>   reader->Update();
>   system("pause");
>   std::cout<<pngIO->GetImageSizeInBytes()<<" "<<512*512<<std::endl;
>   std::cout<<pngIO->GetIORegion()<<std::endl;
> //===============================================Writer
> Part=============================================
>   itk::VTKImageIO::Pointer vtkIO=itk::VTKImageIO::New();
>   vtkIO->SetFileTypeToBinary();
>   vtkIO->SetNumberOfDimensions(3);
>   vtkIO->SetNumberOfComponents(1);
>   vtkIO->SetDimensions(0,512);
>   vtkIO->SetDimensions(1,512);
>   vtkIO->SetDimensions(2,259);
>   vtkIO->SetSpacing(0,1);
>   vtkIO->SetSpacing(1,1);
>   vtkIO->SetSpacing(2,2.23776);
>   writer->SetImageIO(vtkIO);
>
>   writer->SetFileName( outputFilename );
>   writer->SetInput( reader->GetOutput() );
>   try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & err )
>     {
>     std::cerr << "ExceptionObject caught !" << std::endl;
>     std::cerr << err << std::endl;
>     return EXIT_FAILURE;
>     }
>   std::cout<<vtkIO->GetIORegion()<<std::endl;
> //==========================================Visualizing
> Part===============================================
>
>   vtkStructuredPointsReader* vtkReader=vtkStructuredPointsReader::New();
>   vtkReader->SetFileName("h1-1.vtk");
>   vtkReader->Update();
>
>   vtkContourFilter *iso=vtkContourFilter::New();
>   iso->SetInputConnection(vtkReader->GetOutputPort());
>   iso->SetValue(0,128.0f);
>
>   vtkRenderer* ren=vtkRenderer::New();
>   vtkRenderWindow* renWin=vtkRenderWindow::New();
>   renWin->AddRenderer(ren);
>
>   vtkPolyDataMapper* volumeMapper=vtkPolyDataMapper::New();
>   volumeMapper->SetInputConnection(iso->GetOutputPort());
>   volumeMapper->ScalarVisibilityOff();
>
>   vtkRenderWindowInteractor* iren=vtkRenderWindowInteractor::New();
>   vtkActor* isoActor=vtkActor::New();
>   isoActor->SetMapper(volumeMapper);
>
>   vtkProperty* prop=vtkProperty::New();
>   prop->SetColor(0,1,0);
>
>   isoActor->SetProperty(prop);
>   isoActor->ApplyProperties();
>
>   ren->AddActor(isoActor);
>
>   iren->SetRenderWindow(renWin);
>   renWin->SetSize(400,400);
>   iren->Initialize();
>   iren->Start();
>
>   return EXIT_SUCCESS;
> }
>
>
>
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