[Insight-users] Median filter on Volume: Performance

[Gaëtan Lehmann]

Hi Mark,

What is the image size you are trying to filter?

Please make sure that your application is built in Release mode - this  
can make a HUGE difference.

For the efficiency and the spherical neighborhood, you may want to try  
the RankImageFilter which is in the Review directory.
For large neighborhoods, it may improve significantly the performance.

Regards,

Gaëtan



Le 23 févr. 11 à 14:36, sacrif a écrit :

>
> Hello!
>
> Actually I simply want to load a volume, run a median filter on it  
> and write
> the resulting volume back to disk. Therefore I implemented the  
> following
> code:
>
>
> typedef signed short PixelType;
> static const unsigned int Dimension = 3;
> typedef itk::Image<PixelType, Dimension> InputImageType;
> typedef itk::Image<PixelType, Dimension> OutputImageType;
> typedef itk::ImageFileReader<InputImageType> ReaderType;
> typedef itk::ImageFileWriter< InputImageType >  WriterType;
> typedef itk::MedianImageFilter< InputImageType, OutputImageType >
> MedianFilterType;
>
> void MyClass::createMedianHdrFile(std::string filename)
> {
> 	ReaderType::Pointer reader = ReaderType::New();
> 	reader->SetFileName(filename.c_str());
>
> 	MedianFilterType::Pointer medianFilter = MedianFilterType::New();
> 	InputImageType::SizeType indexRadius;
> 	indexRadius[0] = 10; // radius along x
> 	indexRadius[1] = 10; // radius along y
> 	indexRadius[2] = 10; // radius along z
> 	medianFilter->SetRadius( indexRadius );
> 	medianFilter->SetInput(reader->GetOutput());
>
> 	std::string fnNoEnding = getFilenameWithErasedEnding(filename,  
> ".hdr");
> 	std::string fnNewEnding = getFilenameWithNewEnding(fnNoEnding,
> "_Median.hdr");
>
> 	WriterType::Pointer writer = WriterType::New();
> 	writer->SetFileName( fnNewEnding.c_str());
> 	writer->SetInput( medianFilter->GetOutput() );
> 	writer->Update();
> 	cout << "Median End" << endl;
> }
>
>
> Basically this works if I use a very small filter with  
> "indexRadius[0/1/2] =
> 1;". However, as soon as I use "indexRadius[0/1/2] = 10;" the  
> calculation
> seems to take for ever.
> In the meanwhile the program ran for approximately 3 hours and did not
> finish yet. Is it really possible that the calculation of a "median  
> volume"
> takes such a long time? And is there any way to reduce this time span?
>
> My input and output volume are in the Analyze format. For the  
> current test
> run my input and output volume dimensions are  96x96x96 and the  
> filter size
> is 10x10x10. However, I would also like to create "median volumes"  
> of even
> larger data sets and with larger Filter dimensions.
> The test input volume min and max intensity are -1093 and 1086,
> respectively.
>
> Additionally I wanted to ask whether there is a simple way to run  
> apply a
> spherical median filter of a certain radius instead of using the  
> cuboid
> defined by "indexRadius[0/1/2]".
>
> Thank you for your help & Kind regards
> Mark
> -- 
> View this message in context: http://old.nabble.com/Median-filter-on-Volume%3A-Performance-tp30994977p30994977.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
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-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.itk.org
http://www.mandriva.org  http://www.bepo.fr

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