[ITK-users] Deformable Transformation for Coregistration Simple ITK JAVA code

[ivan]

i try with this code

Affine and After BSpline

but after 190 iterations return error code

-------
itk::simple::Transform
 AffineTransform (000000001966EA60)
   RTTI typeinfo:   class itk::AffineTransform<double,3>
   Reference Count: 3
   Modified Time: 3451
   Debug: Off
   Object Name: 
   Observers: 
     none
   Matrix: 
     -0.0283494 0.437495 -0.558782 
     -0.215329 2.14011 2.01216 
     0.661568 -8.35499 1.81576 
   Offset: [0.0377555, -0.0313043, -0.251059]
   Center: [0, 0, 0]
   Translation: [0.0377555, -0.0313043, -0.251059]
   Inverse: 
     -435.991 -81.6103 -43.7342 
     -36.2773 -6.70277 -3.73619 
     -8.07294 -1.10745 -0.706396 
   Singular: 0

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Maximum
number of iterations (200) exceeded.
 Iteration: 200
 Metric value: -0,176593
Exception in thread "main" java.lang.RuntimeException: Exception thrown in
SimpleITK new_BSplineTransform:
..\..\..\..\..\SimpleITK\Code\Common\src\sitkBSplineTransform.cxx:188:
sitk::ERROR: Transform is not of type BSplineTransform!
	at org.itk.simple.SimpleITKJNI.new_BSplineTransform__SWIG_3(Native Method)
	at org.itk.simple.BSplineTransform.<init>(BSplineTransform.java:75)
	at ImageRegistrationMethodNaplab.main(IterationUpdate.java:68)


this is my code



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 ImageRegistrationMethodNaplab {
  public static void main(String argv[]) {
  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }
  
  

  int   ImageDimension = 3;
  char   PixelType;

  
  
  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
  reader.setFileName(argv[0]);
  Image fixed  = reader.execute();
  reader.setFileName(argv[1]);
  Image moving = reader.execute();
  
  
  
  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.AffineTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkBSpline );
  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);
  
  
  org.itk.simple.Transform outTx = R.execute( fixed, moving );
  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());

  outTx.writeTransform(argv[2]);
  
  org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
    
  
  
  
  fixed.getSpacing();
  fixed.getOrigin();
  //fixed.getLargestPossibleRegion();
  fixed.getDirection();
   

 int SplineOrder = 3;
  long SpaceDimension = ImageDimension;
 double CoordinateRepType;
  
  
 
 //org.itk.simple.Transform R = new 
org.itk.simple.BSplineTransform(SpaceDimension,SplineOrder);
 
 

 
  
  //org.itk.simple.BSplineTransformInitializerFilter R = new 
org.itk.simple.BSplineTransformInitializerFilter();
  //R.getTransformDomainMeshSize();
  //R.getOrder();
  
 
  //org.itk.simple.Transform outTx = R.execute(moving);
  
  //org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
  //R2.getDomainOrigin();
  
 
  
  
  
 // IterationUpdate cmd = new IterationUpdate(R);
 // R.addCommand( EventEnum.sitkIterationEvent, cmd);
  

  
  
  

  //getDimension Return the dimension of the Transform ( 2D or 3D )
 // R.setInitialTransform( new
org.itk.simple.BSplineTransform(SplineOrder,SpaceDimension ) );
 //R.getDomainDirection();
 
  //fixed.getDimension()
  
    
  
  System.out.println("-------");
  System.out.println(outTx.toString());
  //System.out.format(" Fixed Initial Transform: %d\n",
R.getFixedInitialTransform());
  //System.out.format(" Moving Initial Transform: %d\n",
R.getMovingInitialTransform());
  //System.out.format(" Initial Transform: %d\n", R.getInitialTransform());
  //System.out.format(" Optimizer Position: %d\n",
R.getOptimizerPosition());
               //System.out.format("Optimizer stop condition: %s\n",
R2.getOptimizerStopConditionDescription());
              //System.out.format(" Iteration: %d\n",
R2.getOptimizerIteration());
                        //System.out.format(" Metric value: %f\n",
R2.getMetricValue());
  //System.out.format(" Interpolator: %f\n", R.getInterpolator());
  //System.out.format(" Translation X", R.getTranslationAlongX());
 // System.out.format(" Translation Y", R.getTranslationAlongY());
  R2.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
   //org.itk.simple.Transform.writeTransform(argv[4]);
  //org.itk.simple.ResampleImageFilter image = new
org.itk.simple.ResampleImageFilter();
  //image.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
 // image.getOutputPixelType(); 
 // image.getSize ();
  //ImageFileWriter writer = new ImageFileWriter();
 // writer.setFileName(argv[5]);
    org.itk.simple.Transform transform = new org.itk.simple.Transform();
  reader.setFileName(argv[2]);
  // Write result image
  ImageFileWriter writer2 = new org.itk.simple.ImageFileWriter();
  writer2.setFileName(argv[3]);
  
  
  
  org.itk.simple.ResampleImageFilter transf = new 
org.itk.simple.ResampleImageFilter();
    transf.setReferenceImage(fixed);
  transf.setTransform(outTx);
  transf.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
  //InterpolatorEnum interp = 
		  transf.getInterpolator();
  //transf.setInterpolator(interp);
//  VectorDouble orig = 
		  transf.getOutputOrigin();
  //VectorDouble spac = 
		  transf.getOutputSpacing();
 // VectorDouble dir = 
		  transf.getOutputDirection();
  //Double pix = 
		  transf.getDefaultPixelValue();
  //transf.setInterpolator(dir);
  //VectorUInt32 pts = new VectorUInt32();
  transf.getSize();
  transf.execute(moving);
   Image blurredImg = transf.execute(moving);
    //Image castImg = caster.execute(blurredImg);
    ImageFileWriter writer3 = new ImageFileWriter();
    writer3.setFileName(argv[3]);
     writer3.execute(blurredImg);
     //writer.execute(transform.getResultImage()); 
     // transform.setParameters(reader.execute());
      //Image transform = reader.execute();
  //Transform.setParameters();
    // Perform warp
//  transform.logToConsoleOn();
 // transform.execute();
    }  
}




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