[vtkusers] Re: reading row 3D voxel data

[kurt]

Hi Jens,

As far as I know, there is not a conveniet way to do so, correct me if I am wrong.
However, 'coz ITK support many formats 3D images, I use ITK to read the images at first, then convert them to vtkImageData. The code is enclosed.

Please note, what u need to do is adding headers for the *.img (the raw data). the headers supported by ITK are *.mha and *.hdr.
The former u can find details from ITK's documents. but it is fairly simple, something like that:
NDims = 3 
DimSize = 256 256 63 
ElementType = MET_UCHAR 
ElementSpacing = 1.0 1.0 1.0
ElementByteOrderMSB = False
ElementDataFile = 1.img

u can make the *.hdr using MRIcro, u may download it from www.mricro.com.

The former is simpler, but I recommand the later header, it is more convenient to use.

Good luck!

Kurt Zhao

bool MyImage::ImgReader(vtkImageData * vtkImage, const char * ImgFileName)
{
 typedef unsigned short SegPixelType;
 typedef itk::Image< SegPixelType, Dimension >   ImageType;

 typedef itk::ImageFileReader< ImageType >  ImageReaderType;
 
 ImageReaderType::Pointer    ImageReader     =  ImageReaderType::New();
 ImageReader->SetFileName(  ImgFileName );
 std::cout<< "Reading the image "<< ImageReader->GetFileName()<<"......"<<std::endl; 
 
 try 
    {
     ImageReader->Update();
    }
 catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception Caught !" << std::endl;
    std::cerr << excep << std::endl;
    }
 ImageReader->GetOutput()->ReleaseDataFlagOn();
 ImageType *itkImg=ImageReader->GetOutput();
 

 typedef itk::VTKImageExport<ImageType> ImageExportType;
 ImageExportType::Pointer itkExporter = ImageExportType::New();
 itkExporter->SetInput(itkImg);

 
 vtkImageImport* vtkImporter = vtkImageImport::New();  
    ConnectPipelines(itkExporter, vtkImporter);
 vtkImporter->Update();
 vtkImageData *tImage=vtkImporter->GetOutput();
 vtkImage->DeepCopy(tImage);
 vtkImage->SetSpacing(1,1,1);
// vtkImage->Print(std::cout);
 vtkImporter->Delete();
 return false;
}

template <typename ITK_Exporter, typename VTK_Importer> 
void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
{
 // importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
 // importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
 importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
  importer->SetSpacingCallback(exporter->GetSpacingCallback());
  importer->SetOriginCallback(exporter->GetOriginCallback());
  importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
  importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
  importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
  importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
  importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
  importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
  importer->SetCallbackUserData(exporter->GetCallbackUserData());
}








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Today's Topics:

   1. reading row 3D voxel data (Jens Frederich)
   2. reading row 3D voxel data (Jens Frederich)
   3. reading row 3D voxel data (Jens Frederich)


----------------------------------------------------------------------

Message: 1
Date: Wed, 7 Jan 2004 20:27:09 +0100
From: Jens Frederich < jfrederich at mac.com> 
Subject: [vtkusers] reading row 3D voxel data
To: vtk < vtkusers at vtk.org> 
Message-ID: < 7C576394-4147-11D8-A56E-000A95A0B65C at mac.com> 
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi all,

what is the best class (way) for reading 3D binary row voxel data. The 
data is saved in one file, not many 2D images. I would do volume 
rendering, isosurface, contour etc with this data.
With the volume rendering library vgl 
(http://www.volumegraphics.com/products/vgl/index.html) is this very 
simple. Here a code sample:

VGLSampleGridData* volumeData = new VGLSampleGridData (VGL_TYPE_UINT16);
  // load voxel data:
   VGLSampleGridIO* importPlugIn = VGLSampleGridIO::create ("raw");
   importPlugIn-> setHeaderSkip (40);
   imortPlugIn-> setSampleGridSize (VGLSampleGridSize (42,42,42));
   importPlugIn-> setSampleGridSize (VGLSampleGridSize (250,250,1));
   importPlugIn-> setSampleDataType (VGL_TYPE_UINT16);
   importPlugIn-> open ("../data/simdata4.vol");
   importPlugIn-> read (volumeData);
   importPlugIn-> close ();
   delete importPlugIn;

It's very easy. But I search the same on vtk please.
Thanks for help.

Best regards,
Jens
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