[Insight-users] watershed segmentation in own function

[Ella Maria Kadas]

Hi, I had a similar problem and that was in my case because the input i was giving the writer was an empty image. I would suggest that u make an reader->Update(), before u initialize the output image.Cheers,Ella

--- G G <greenlander1986 at gmail.com> schrieb am Di, 1.3.2011:

Von: G G <greenlander1986 at gmail.com>
Betreff: [Insight-users] watershed segmentation in own function
An: "insight-users" <insight-users at itk.org>
Datum: Dienstag, 1. März, 2011 12:17 Uhr

Hi Luis,
I tried to write funcion, which return image after image segmentation. I have this code:

        typedef float              PixelType;
        const   unsigned int                      InputDimension = 3;


        typedef itk::Image< PixelType,  InputDimension >     ImageType;
        typedef  itk::ImageFileReader< ImageType >   ReaderType;

        ReaderType::Pointer reader = ReaderType::New();

        reader->SetFileName( this->settings.getInputPath().c_str() );

        const   unsigned int                      OutputDimension = 3;

        typedef itk::RGBPixel<unsigned char>      RGBPixelType;    // ws

        typedef itk::Image< RGBPixelType, OutputDimension >  OutputImageType; // ws

        WriterType::Pointer writer = WriterType::New();
        writer->SetFileName( this->settings.getOutputPath().c_str() );


        OutputImageType::Pointer output = OutputImageType::New();
            output = this->segmentationCC<OutputImageType::Pointer, ImageType, OutputImageType, ImageType::Pointer>(reader->GetOutput());

        writer->SetInput(output);
        try
        {
            writer->Update();
            //writer->UpdateLargestPossibleRegion();
            //writer->UpdateOutputData(output);            

        }
        catch (itk::ExceptionObject &e)
        {
            this->settings.setLogMessage("Chyba pri zapisu do souboru");
            cerr << e << endl;
            this->settings.setIsOK(false);

            return;
        }


then I have to show function segmentationCC:

    template<typename TOutputImageTypePointer, typename TImageType, typename TRGBImageType, typename TInput> TOutputImageTypePointer IOCompute::segmentationCC(TInput input)

    {
          typedef   itk::GradientMagnitudeRecursiveGaussianImageFilter< TImageType, TImageType > GradientMagnitudeFilterType;
          GradientMagnitudeFilterType::Pointer gradienMagnitudeFilter = GradientMagnitudeFilterType::New();

          gradienMagnitudeFilter->SetInput( input );
          gradienMagnitudeFilter->SetSigma( 1.0 );


          typedef  itk::WatershedImageFilter< TImageType > WatershedFilterType;
          WatershedFilterType::Pointer watershedFilter = WatershedFilterType::New();

          watershedFilter->SetInput( gradienMagnitudeFilter->GetOutput() );
          watershedFilter->SetThreshold( 0.01 );
          watershedFilter->SetLevel(     0.15 );

          typedef itk::Functor::ScalarToRGBPixelFunctor< unsigned long > ColorMapFunctorType;


          typedef WatershedFilterType::OutputImageType  LabeledImageType;

          typedef itk::UnaryFunctorImageFilter<
                                        LabeledImageType,
                                        TRGBImageType,

                                        ColorMapFunctorType
                                                        > ColorMapFilterType;

          ColorMapFilterType::Pointer colorMapFilter = ColorMapFilterType::New();


          colorMapFilter->SetInput(  watershedFilter->GetOutput() );

          TOutputImageTypePointer output = colorMapFilter->GetOutput();
          return output;
    }



when I use writer->Update();

I have exception


itk::ExceptionObject (00A3F388)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<class itk::RGBPixel<unsigned char>,3> >::Write(void)" 
File: c:\itkrel\src\insight\code\io\itkImageFileWriter.txx

Line: 271
Description: itk::ERROR: ImageFileWriter(00B513B8): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (00A3F3F8)
  Dimension: 3
  Index: 0 0 0 
  Size: 0 0 0 

Largest possible region: ImageRegion (00A3F3DC)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [0, 0, 0]


or when I have writer->UpdateLargestPossibleRegion(); then no exception, but any writter output file :'-(


Please help me or give some advice, I am desperate...
Thanks a lot


-----Integrierter Anhang folgt-----

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.html

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20110301/2511e2d3/attachment.htm>