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

[ivan]

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 ); 
}


}
}












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