[ITK] [ITK-users] Simple ITK Overlap Two Image for example PET and MRI or CT ?? is it possible? and Image Fusion?

ivan ivan.granata.na at gmail.com
Fri Nov 11 02:43:43 EST 2016


ok i'm thank u

but really i see overlap not fusion


this is my code and my result

import org.itk.simple.*;


class IterationUpdate  extends Command {

	  private ImageRegistrationMethod m_Method;

	  public IterationUpdate(ImageRegistrationMethod m) {
	    super();
	    m_Method=m;
	  }

	  public void execute() {
	    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
	    System.out.format("%3d = %10.5f : [%f, %f]\n",
	                      m_Method.getOptimizerIteration(),
	                      m_Method.getMetricValue(),
	                      pos.get(0), pos.get(1));
	  }
	}

class ImageFusionFinal {

  public static void main(String argv[]) {

  //if ( argv.length < 3 )
   // {
  //    System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethod1");
   //   System.exit(-1);
  //  }


	//-----------Read
Image----------------------------------------------------------------------------------------------------	 	  
			    org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
			  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32);
			  reader.setFileName("D:/workspace/ImageFusionFinal/img/CT.nii");
			  Image ctimage  = reader.execute();
			  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32);
			  reader.setFileName("D:/workspace/ImageFusionFinal/img/PET.nii");
			  Image petimage = reader.execute();
			  
			  System.out.format("Images Read\n");
			 // println("Images Read"); 
	
//------Initial
Transform---------------------------------------------------------------------------------------------------------	  
	
org.itk.simple.CenteredTransformInitializerFilter initialTx = new
org.itk.simple.CenteredTransformInitializerFilter();
org.itk.simple.Transform tx = initialTx.execute( ctimage, petimage, new
org.itk.simple.AffineTransform(ctimage.getDimension()) );


//------Registration
Method---------------------------------------------------------------------------------------------------------	  



org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
			  R.setMetricAsMattesMutualInformation();
			 // double maxStep = 4.0;
			 // double minStep = 0.01;
			 // int numberOfIterations = 200;
			 // double relaxationFactor = 0.5;
			//  R.setOptimizerAsRegularStepGradientDescent( maxStep,
			                                            //  minStep,
			                                           //   numberOfIterations,
			                                          //    relaxationFactor );
			  
			  R.setInitialTransform( new org.itk.simple.Euler3DTransform() );
			  
	
			  
			  double learningRate = 1 ;
			  long numberOfIterations = 100;
			  long numberOfHistogramBins = 50;
			  
			  R.setMetricAsMattesMutualInformation(numberOfHistogramBins);
			 
R.setOptimizerAsGradientDescentLineSearch(learningRate,numberOfIterations);
			  R.setOptimizerScalesFromIndexShift();
			  VectorUInt32 pts1 = new VectorUInt32(3);
			  // org.itk.simple.VectorUInt32 pts1;
			   pts1.clear();
			   pts1.push_back(4);
			   pts1.push_back(2);
			   pts1.push_back(1);
			    
			  
			   R.setShrinkFactorsPerLevel(pts1);
			 
			   
			   VectorDouble pts2 = new VectorDouble(3);

			   /* seed points */
			   pts2.clear();
			   pts2.push_back(8);
			   pts2.push_back(4);
			   pts2.push_back(2);
			   System.out.println(pts2);
			     R.setSmoothingSigmasPerLevel(pts2);
			     
			  
			  R.smoothingSigmasAreSpecifiedInPhysicalUnitsOn();
			  
			 
R.setMetricSamplingStrategy(org.itk.simple.ImageRegistrationMethod.MetricSamplingStrategyType.RANDOM);
			 
			  R.setMetricSamplingPercentage(0.1);
			  R.setInitialTransform(tx);
			  R.setInterpolator( InterpolatorEnum.sitkLinear );
			  
			  
			  
			  
			
			  IterationUpdate cmd = new IterationUpdate(R);
			  R.addCommand( EventEnum.sitkIterationEvent, cmd);
			  
			  org.itk.simple.Transform outTx = R.execute( ctimage, petimage );
			  
			  System.out.println("-------");
			  System.out.println(outTx.toString());
			  
			  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
			  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
			  System.out.format(" Metric value: %f\n", R.getMetricValue());
			  
			  
			  
			  
			  
			  
			  
			  //tx.AddTransform(sitk.Transform(3,sitk.sitkAffine));
			  R.setInitialTransform(outTx,true);
			  tx.addTransform ( R.execute( ctimage, petimage ));
			  
			  double learningRate2 = 1 ;
			  long numberOfIterations2 = 100;
			  //long numberOfHistogramBins2 = 50;
			  
			 
			 
R.setOptimizerAsGradientDescentLineSearch(learningRate2,numberOfIterations2);
			  R.setOptimizerScalesFromIndexShift();
			  VectorUInt32 pts3 = new VectorUInt32(2);
			  // org.itk.simple.VectorUInt32 pts1;
			  pts3.clear();
			  pts3.push_back(2);
			  pts3.push_back(1);
			  	  
			   R.setShrinkFactorsPerLevel(pts3);
			 
			   
			   VectorDouble pts4 = new VectorDouble(2);

			   /* seed points */
			   pts4.clear();
			   pts4.push_back(4);
			   pts4.push_back(1);
			   System.out.println(pts4);
			     R.setSmoothingSigmasPerLevel(pts4);
			     R.setInitialTransform(tx);
			     
			     
			     
			     
			  R.smoothingSigmasAreSpecifiedInPhysicalUnitsOn();
			  
			 
R.setMetricSamplingStrategy(org.itk.simple.ImageRegistrationMethod.MetricSamplingStrategyType.RANDOM);
			 
			  R.setMetricSamplingPercentage(0.1);
			  R.setInitialTransform(tx);
			  R.setInterpolator( InterpolatorEnum.sitkLinear );
			  
			  
//------Resample
Method---------------------------------------------------------------------------------------------------------	  
	  
			  
			  
			  org.itk.simple.ResampleImageFilter resample = new 
org.itk.simple.ResampleImageFilter();
			  resample.setReferenceImage(ctimage);
			  
			  resample.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
			  //InterpolatorEnum interp = 
			  resample.setInterpolator(InterpolatorEnum.sitkBSpline);
			  resample.setTransform(outTx);
			  //transf.setInterpolator(interp);
			//  VectorDouble orig = 
			  resample.getOutputOrigin();
			  //VectorDouble spac = 
			  resample.getOutputSpacing();
			 // VectorDouble dir = 
			  resample.getOutputDirection();
			  //Double pix = 
			  resample.getDefaultPixelValue();
			  //transf.setInterpolator(dir);
			  //VectorUInt32 pts = new VectorUInt32();
			  resample.getSize();
			  resample.execute(petimage);
			  Image out  = resample.execute(petimage);
			  
//------Resample
Method---------------------------------------------------------------------------------------------------------	  
	  
			  
			  ComposeImageFilter out_fin = new ComposeImageFilter();
			 Image out_fin2 = out_fin.execute(ctimage, petimage);
			  
			  
			 // org.itk.simple.CheckerBoardImageFilter out_fin = new 
org.itk.simple.CheckerBoardImageFilter();
			  
			  
			//  out_fin.execute(ctimage, petimage);
			 
			 VectorUInt32 checkerPattern = new VectorUInt32(2);
			  // org.itk.simple.VectorUInt32 pts1;
			 checkerPattern.clear();
			 checkerPattern.push_back(8);
			 checkerPattern.push_back(8);
			 checkerPattern.push_back(1);
			 
			 CheckerBoardImageFilter out_fin3 = new CheckerBoardImageFilter();
			 Image out_fin4 = out_fin3.execute(ctimage, petimage,checkerPattern);
			  
			 
			 
			// LabelOverlayImageFilter out_fin5 = new LabelOverlayImageFilter();
			 
			// org.itk.simple.Image petimage2 = new 
org.itk.simple.Image(ctimage.getSize(), PixelIDValueEnum.sitkVectorFloat64);
			// petimage2.copyInformation(ctimage);
			// Image out_fin6 = out_fin5.execute(ctimage, petimage2);
			 
			 
			  
//-----Write Fused
Image---------------------------------------------------------------------------------------------------------	  
	  
			  
			  //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[1]);
			//  writer.execute( castImg ); 
			  
			  
			  
			  
			  
			  //Image blurredImg = resample.execute(out_fin2);
			    //Image castImg = caster.execute(blurredImg);
			    ImageFileWriter writer3 = new ImageFileWriter();
			   
writer3.setFileName("D:/workspace/ImageFusionFinal/img/CT_PET_Fusion2.nii");
			    writer3.useCompressionOn();
			     writer3.execute(out_fin4);
			     //writer.execute(transform.getResultImage()); 
			     // transform.setParameters(reader.execute());
			      //Image transform = reader.execute();
			  //Transform.setParameters();
			    // Perform warp
			//  transform.logToConsoleOn();
			 // transform.execute();
			  
			  
  }
	
  }


<http://itk-users.7.n7.nabble.com/file/n37760/CT.jpg> 
<http://itk-users.7.n7.nabble.com/file/n37760/PET.jpg> 

result

<http://itk-users.7.n7.nabble.com/file/n37760/CT_PET_Fusion.jpg> 



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