Hi Ahmed,
the issue with OsiriX is very likely that vmtk is probably built against one
version of VTK/ITK,
while OsiriX incorporates a different version. If have to make sure OsiriX and
vmtk link
to the same VTK and ITK libraries.
An alternative would be to write vmtk code as an external executable that you
can then
invoke as an external process from within your OsiriX plugin. You'll need to
write the
images to disk to pass them from OsiriX to vmtk and back, but at least you
won't have
the linking issue.
Hope this helps.
Luca
On Feb 6, 2013, at 7:01 PM, Ahmed Harouni wrote:
>
> Dear Luca
>
> Thanks for your efforts and making VMTK available. I downloaded it and used
> it from python on some of the MRI data we have and the results are great. Now
> I want to call it directly for some Osirix plugins that I wrote previously. I
> downloaded VMTK Source and complied it on Mac OSX Lion 10.7.5. I linked it
> with my 64bit plugin written for Osirix 5.5.2.
> I am getting errors of bad memory access when trying to use
> vtkvmtkVesselnessMeasureImageFilter using
> vtkvmtkVesselnessMeasureImageFilter
> *myvessel=vtkvmtkVesselnessMeasureImageFilter::New()
>
> I and a newbie to VMTK but I think I need to initialize the filter with my
> image pixel type and size as used in ITK (see below). Could you please point
> me to some examples or the right classes to use as the help found online is
> limited to information found in the header files.
>
> Thanks for your help
>
> Ahmed A. Harouni
>
> long size = sizeof(float) * imageWidth * imageHeight * imageAmount;
> const unsigned int Dimension = 3;
> typedef float InputPixelType;
> typedef float OutputPixelType;
> typedef itk::Image< InputPixelType, Dimension > InputImageType;
> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> typedef itk::HessianRecursiveGaussianImageFilter<InputImageType >
> HessianFilterType;
> typedef itk::Hessian3DToVesselnessMeasureImageFilter<OutputPixelType >
> VesselnessMeasureFilterType;
> typedef itk::ImportImageFilter< InputPixelType, Dimension > ImportFilterType;
> ImportFilterType::Pointer importFilter;
> importFilter = ImportFilterType::New();
> ImportFilterType::SizeType itksize;
> itksize[0] = imageWidth; // size along X
> itksize[1] = imageHeight; // size along Y
> itksize[2] = imageAmount;// size along Z
> ImportFilterType::IndexType start;
> start.Fill( 0 );
> ImportFilterType::RegionType region;
> region.SetIndex( start );
> region.SetSize( itksize );
> importFilter->SetRegion( region );
> double origin[ 3 ];
> origin[0] = 0; // X coordinate
> origin[1] = 0; // Y coordinate
> origin[2] = 0; // Z coordinate
> importFilter->SetOrigin( origin );
> double spacing[ 3 ];
> spacing[0] = imgspacing[0]; // along X direction
> spacing[1] = imgspacing[1]; // along Y direction
> spacing[2] = imgspacing[2]; // along Z direction
> importFilter->SetSpacing( spacing );
> const bool importImageFilterWillOwnTheBuffer = false;
> importFilter->SetImportPointer( inData, itksize[0] * itksize[1] * itksize[2],
> importImageFilterWillOwnTheBuffer);
> NSLog(@"ITK Image allocated");
> HessianFilterType::Pointer hessianFilter = HessianFilterType::New();
> VesselnessMeasureFilterType::Pointer vesselnessFilter =
> VesselnessMeasureFilterType::New();
> hessianFilter->SetNormalizeAcrossScale(true);
> hessianFilter->SetInput( importFilter->GetOutput() );
> vesselnessFilter->SetInput( hessianFilter->GetOutput() );
> vesselnessFilter->SetAlpha1(0.5);
> vesselnessFilter->SetAlpha2(0.5);
> float m_sigma;
> size = imageWidth * imageHeight * imageAmount;//-4 to protect memory overflow
> when using vec_max
> for(m_sigma=startscale;m_sigma<=endscale;m_sigma+=scalestep)
> {
> hessianFilter->SetSigma(m_sigma);
> try
> {
> vesselnessFilter->Update();
> }
>
>
>
>
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