[ITK] [ITK-users] SimpleITK JAVA ImageSeriesReader and PatchBasedDenoisingImageFilter and 4d images

[Lowekamp, Bradley (NIH/NLM/LHC) [C]]

I would look at the python examples and usage for reference:

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader.py
https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader2.py

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/CMakeLists.txt#L73-L89

HTH,
Brad

> On Oct 6, 2016, at 8:32 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> hi 
> 
> can anyone help me how to write ImageSeriesReader in Java with simple itk
> 
> i wolud read a dicom series in a path and after apply a
> PatchBasedDenoisingImageFilter
> 
> if possible i would work also with 4d image (multicomponent filter)
> 
> 
> thx
> 
> 
> this is my code
> 
> import org.itk.simple.*;
> 
> import java.util.Vector; 
> class PatchBasedDenoisingImageFilter {
> public static void main(String argv[]) {
> 		
> 	if ( argv.length < 5 ) {
> System.out.println("Immetti prima:  <input_img> <patch_radius> <smoothness>
> <patch_number> <noise_sigma> <output_img>");
> return;
> }
> 
> org.itk.simple.ImageSeriesReader reader = new
> org.itk.simple.ImageSeriesReader();
> 
> VectorString inputdicom = new VectorString();
> inputdicom.toString(argv[0]);
> reader.setFileNames(inputdicom);
> 
> 
> //reader.setVectorString (argv[0]);
> //reader.setFileNames(inputdicom);
> 
> 
> Image img = reader.execute();
> 
> System.out.println(img.getDimension());
> 
> org.itk.simple.PatchBasedDenoisingImageFilter filter = new
> org.itk.simple.PatchBasedDenoisingImageFilter();
> 
> filter.getAlwaysTreatComponentsAsEuclidean ();
> boolean setKBE = false;
> filter.setKernelBandwidthEstimation ( setKBE );
> //filter.getKernelBandwidthUpdateFrequency ();
> //filter.getKernelBandwidthFractionPixelsForEstimation ();
> //filter.getKernelBandwidthMultiplicationFactor ();
> //filter.getKernelBandwidthSigma ();
> filter.setNoiseModel(org.itk.simple.PatchBasedDenoisingImageFilter.NoiseModelType.GAUSSIAN);
> filter.getNumberOfIterations (); //cablato
> filter.getSampleVariance ();
> filter.setPatchRadius ( Long.valueOf ( argv[1] ).longValue() );
> filter.setNoiseModelFidelityWeight ( Double.valueOf ( argv[2]
> ).doubleValue() );
> 
> if ( argv.length < 5 ) filter.getNumberOfSamplePatches ();
> else filter.setNumberOfSamplePatches ( Long.valueOf ( argv[3] ).longValue()
> );
> 
> if ( argv.length < 6 ) 
> 	filter.getNoiseSigma ();
> else filter.setNoiseSigma (Double.valueOf ( argv[4] ).doubleValue() );
> 
> Image blurredImg  = filter.execute(img);
> 
> CastImageFilter caster = new CastImageFilter();
> caster.setOutputPixelType( img.getPixelIDValue() );
> Image castImg = caster.execute( blurredImg );
> ImageFileWriter writer = new ImageFileWriter();
> 
> writer.setFileName(argv[5]);
> writer.execute( castImg ); 
> }
> 
> 
> }
> }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-JAVA-ImageSeriesReader-and-PatchBasedDenoisingImageFilter-and-4d-images-tp37645.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
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