[Insight-users] RelabelComponentImageFilter nothing at rendered window..,

[Luis Ibanez]

Hi Yasser,

The Relabel image filter assigns values like : 1,2,3....

to the pixels in the image.  Those values will
appear very dark in any viewer unless you rescale
them before attempting to visualize them.

http://www.itk.org/Insight/Doxygen/html/classitk_1_1RelabelComponentImageFilter.html


Since you are using VTK for visualization, you simply
need to adjust the parameters of intensity windowing
in your viewer.



   Regards,


     Luis


----------------------
yasser salman wrote:
> Hi All..,
> 
> when i'm using  itkRelabelComponentImageFilter as the
> input to the writer the file saved and i can display
> it clearly also GetSizeOfObjectsInPixels() works good,
> but when i'm using it as the input of of
> itk2vtkconnector nothing displayed in the render
> window can u find out why?
> 
> 
>  typedef unsigned short   InputPixelType;
>   typedef float        InternalPixelType;
>   
>   typedef unsigned short   SegmentedPixelType;
> 
>   typedef itk::Image< InputPixelType, 3 >        
> InputImageType;
>   typedef itk::Image< InternalPixelType, 3>      
> InternalImageType;
> 
>   typedef itk::Image< SegmentedPixelType, 3 >    
> SegmentedImageType;
> 
>   typedef   itk::CastImageFilter< 
>                  InputImageType, 
>                  InternalImageType >    
> CastImageFilterType;
> 
>   typedef   itk::CurvatureFlowImageFilter< 
>                  InternalImageType, 
>                  InternalImageType >    
> CurvatureFlowImageFilterType;
> 
>   typedef   itk::ConfidenceConnectedImageFilter< 
>                          InternalImageType, 
>                          SegmentedImageType >     
> 				 ConfidenceConnectedImageFilterType;
> 
>   typedef itk::ConnectedThresholdImageFilter< 
> 			InternalImageType, SegmentedImageType >
> ConnectedFilterType;
>   
> 
>   typedef itk::ImageToVTKImageFilter<
> SegmentedImageType >  
> 			ITK2VTKConnectorFilterType;
> 
>   typedef itk::VTKImageToImageFilter< InputImageType  
>   >  
>             VTK2ITKConnectorFilterType;
> 	   typedef itk::ImageSeriesReader< InputImageType >  
>   ReaderType;
>   typedef std::vector<std::string> seriesIdContainer;
>   typedef std::vector<std::string> fileNamesContainer;
>   typedef ConnectedFilterType::IndexType IndexType;	
>   typedef
> itk::ImageMomentsCalculator<SegmentedImageType>
> ImageMomentsType;
> typedef itk::ImageSeriesReader< InputImageType >    
> ReaderType;
> 
>   itk::DICOMImageIO2::Pointer dicomIO =
> itk::DICOMImageIO2::New();
> 
>   // Get the DICOM filenames from the directory
>   itk::DICOMSeriesFileNames::Pointer nameGenerator =
> itk::DICOMSeriesFileNames::New();
>  CString  directoryname(VolData_FName);
> 
>   std::string    stringdirectory =
> directoryname.GetBuffer(200);
> 
>  // nameGenerator->SetDirectory(  stringdirectory );
> it works!!!!!
> 
>   nameGenerator->SetDirectory(
> "D:/imagedata/Dicom/shy4" );
> 
>   typedef std::vector<std::string> seriesIdContainer;
>   const seriesIdContainer & seriesUID =
> nameGenerator->GetSeriesUIDs();
> seriesIdContainer::const_iterator seriesItr =
> seriesUID.begin();
>   seriesIdContainer::const_iterator seriesEnd =
> seriesUID.end();
>   while( seriesItr != seriesEnd )
>     {
>     std::cout << seriesItr->c_str() << std::endl;
>     seriesItr++;
>     }
>   
>   typedef
> itk::RelabelComponentImageFilter<SegmentedImageType,SegmentedImageType>
> RelabelImageFilter;
>   typedef std::vector<std::string> fileNamesContainer;
>   fileNamesContainer fileNames;
>    fileNames = nameGenerator->GetFileNames();
>   
>   
>   ReaderType::Pointer reader = ReaderType::New();
>   reader->SetFileNames( fileNames );
>   reader->SetImageIO( dicomIO );
> 
>     reader->Update();
>   
> 
>   CastImageFilterType::Pointer cast =
> CastImageFilterType::New();
> 
>   CurvatureFlowImageFilterType::Pointer smoothing = 
> CurvatureFlowImageFilterType::New();
> 
>   ConfidenceConnectedImageFilterType::Pointer
> confidence = 
> ConfidenceConnectedImageFilterType::New();
> 
>   ConnectedFilterType::Pointer connectedThreshold = 
> ConnectedFilterType::New();
>   RelabelImageFilter::Pointer rcfilter=
> RelabelImageFilter::New();
>   VTK2ITKConnectorFilterType::Pointer VTK2ITKconnector
> = 
> VTK2ITKConnectorFilterType::New();
> 
>   
> 
>   cast->SetInput( reader->GetOutput() );
> 
>   smoothing->SetInput(  cast->GetOutput() );
>   confidence->SetInput( smoothing->GetOutput());
> 
>   smoothing->SetTimeStep( 0.0625 );
>  smoothing->SetNumberOfIterations( 2 );
>     connectedThreshold->SetInput(
> smoothing->GetOutput() );
>   connectedThreshold->SetLower(  L_threshold  );
>   connectedThreshold->SetUpper(  H_threshold);
>   connectedThreshold->SetReplaceValue(
> SegmentedRegionColor );
> 
> 
>   typedef ConnectedFilterType::IndexType IndexType;
>   IndexType seed;
>   seed[0] = axi;
>   seed[1] = cron;
>   seed[2] = sag;
> 
>   connectedThreshold->SetSeed( seed );
>   ImageMomentsType::Pointer
> calculator=ImageMomentsType::New();
> connectedThreshold->Update();
>   calculator->SetImage(
> connectedThreshold->GetOutput());
>  calculator->Compute();
> 
> 
>   ITK2VTKConnectorFilterType::Pointer ITK2VTKconnector
> = 
> ITK2VTKConnectorFilterType::New();
> rcfilter->SetInput(connectedThreshold->GetOutput());
> rcfilter->Update();
> 	unsigned long nObjects =
> rcfilter->GetNumberOfObjects();
> 	const std::vector<unsigned long> sizeOfObjects =
> rcfilter->GetSizeOfObjectsInPixels();
> 	std::vector<unsigned long>::const_iterator it;
> 
> 	int i;
> 	 it =  sizeOfObjects.begin();  	
> 	typedef itk::ImageFileWriter<SegmentedImageType>		
> itkWriterType;
> 	typedef itk::DICOMImageIO2									
> itkMetaImageIOType;
> 	itkMetaImageIOType::Pointer		labellerMetaWriterIO  =
> itkMetaImageIOType::New();
> 	 itkWriterType::Pointer				relabellerWriter				=
> itkWriterType::New();
> 	itkMetaImageIOType::Pointer		relabellerMetaWriterIO 
> = itkMetaImageIOType::New();
> 	relabellerWriter->SetInput( rcfilter->GetOutput() );
> 	relabellerWriter->SetFileName(
> "c:/Shapes_relabelled.vtk" );
> 	relabellerWriter->SetImageIO( labellerMetaWriterIO );
> 	relabellerWriter->Write();
> 
> 
> 
>   ITK2VTKconnector->SetInput(connectedThreshold
> ->GetOutput());  //the region displayed ok but if
> rcfilter instead of connectedtehreshold nothing
> displayed..
>  
> ITK2VTKconnector->GetImporter()->SetDataScalarTypeToUnsignedChar();
> 
> /////To the Vtk pipeline...
> 
> 
> 
> 	
> 		
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