[Insight-users] DeformableRegistration8.cxx Works in C++, but Java version does not

[sumit shah]

Dear Itk Users:

I'm a bit confused with the result I've observed.  I have implemented  
example DeformableRegistration8 in java and tested the Java version  
to the CXX version.  I did have to change a few things to get the  
necessary classes wrapped (e.g. itkLBFGSBOptimizer, itkArrayI, etc.)   
I also changed the c++ version to use image type of float instead of  
signed short in order to keep everything as similar as possible.

I ran the c++ version with a command similar to:

DeformableRegistration8 c:/RatLungSlice1.mha c:/RatLungSlice2.mha  
test.mha

and the result is:


Starting Registration
           Probe Tag    Starts    Stops           Time
         Registration           1            1             0.313


I ran the Java version with similar data and got the following result:

ava.lang.RuntimeException: c:\insighttoolkit-2.2.0\code\algorithms 
\itkMattesMutualInformationImageToImageMetric.txx:985:
itk::ERROR: MattesMutualInformationImageToImageMetric(068FB208): Too  
many samples map outside moving image buffer: 11 / 1638

     at  
InsightToolkit.itkImageRegistrationMethodJNI.itkImageRegistrationMethodF 
3F3_Pointer_StartRegistration(Native Method)
     at  
InsightToolkit.itkImageRegistrationMethodF3F3_Pointer.StartRegistration( 
itkImageRegistrationMethodF3F3_Pointer.java:175)
     at edu.ucla.rip.process.RegistrationTestUtils.defregister 
(RegistrationTestUtils.java:125)
     at edu.ucla.rip.process.RegistrationTestUtils.main 
(RegistrationTestUtils.java:131)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke 
(NativeMethodAccessorImpl.java:39)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:585)
     at com.intellij.rt.execution.application.AppMain.main 
(AppMain.java:78)


Here is my config:
WindowsXP SP2,
Visual Studio.NET 2003
JDK1.5
ITK 2.2
CableSWIG CVS

I realize the example I tried was a 2D data set, but the results I  
observe with the 2D dataset are similar to the results I observe with  
some of our internal data sets (i.e. the too many samples map outside  
error).  I just wanted to show an example with the included ITK  
datasets.

My Java source code is at the end of this message.  I'm not sure what  
I am doing wrong, I've checked the source code many times to see if I  
overlooked something, but if I did it is not jumping out at me.  Any  
help that anyone out there can provide will be very much  
appreciated.  Thank you very much.

Sumit



package edu.ucla.rip.process;

import InsightToolkit.itkArrayD;
import InsightToolkit.itkArrayI;
import InsightToolkit.itkBSplineDeformableTransform33;
import InsightToolkit.itkBSplineDeformableTransform33_Pointer;
import InsightToolkit.itkImageFileReaderF3;
import InsightToolkit.itkImageFileReaderF3_Pointer;
import InsightToolkit.itkImageRegion3;
import InsightToolkit.itkImageRegistrationMethodF3F3;
import InsightToolkit.itkImageRegistrationMethodF3F3_Pointer;
import InsightToolkit.itkIterationEvent;
import InsightToolkit.itkJavaCommand;
import InsightToolkit.itkLBFGSBOptimizer;
import InsightToolkit.itkLBFGSBOptimizer_Pointer;
import InsightToolkit.itkLinearInterpolateImageFunctionF3D;
import InsightToolkit.itkLinearInterpolateImageFunctionF3D_Pointer;
import InsightToolkit.itkMattesMutualInformationImageToImageMetricF3F3;
import  
InsightToolkit.itkMattesMutualInformationImageToImageMetricF3F3_Pointer;
import InsightToolkit.itkPointD3;
import InsightToolkit.itkSize3;
import InsightToolkit.itkVectorD3;

/**
* User: sshah
* Date: May 17, 2005
* Time: 12:03:36 PM
*/

public class RegistrationTestUtils {
   public static void defregister(String fix, String mov) throws  
Exception {
     itkImageFileReaderF3_Pointer fixedReader =  
itkImageFileReaderF3.itkImageFileReaderF3_New();
     fixedReader.SetFileName(fix);
     itkImageFileReaderF3_Pointer movingReader =  
itkImageFileReaderF3.itkImageFileReaderF3_New();
     movingReader.SetFileName(mov);

     movingReader.Update();

     final itkLinearInterpolateImageFunctionF3D_Pointer interpolator  
=  
itkLinearInterpolateImageFunctionF3D.itkLinearInterpolateImageFunctionF3 
D_New();
     final itkMattesMutualInformationImageToImageMetricF3F3_Pointer  
metric =  
itkMattesMutualInformationImageToImageMetricF3F3.itkMattesMutualInformat 
ionImageToImageMetricF3F3_New();
     final itkLBFGSBOptimizer_Pointer optimizer =  
itkLBFGSBOptimizer.itkLBFGSBOptimizer_New();
     final itkBSplineDeformableTransform33_Pointer transform =  
itkBSplineDeformableTransform33.itkBSplineDeformableTransform33_New();
     final itkImageRegistrationMethodF3F3_Pointer registration =  
itkImageRegistrationMethodF3F3.itkImageRegistrationMethodF3F3_New();

     registration.SetMetric(metric.GetPointer());
     registration.SetOptimizer(optimizer.GetPointer());
     registration.SetInterpolator(interpolator.GetPointer());
     registration.SetTransform(transform.GetPointer());
     registration.SetFixedImage(fixedReader.GetOutput());
     registration.SetMovingImage(movingReader.GetOutput());
     fixedReader.Update();
     itkImageRegion3 fixedRegion = fixedReader.GetOutput 
().GetBufferedRegion();
     registration.SetFixedImageRegion(fixedRegion);

     itkImageRegion3 bsplineRegion = new itkImageRegion3();
     itkSize3 gridSizeOnImage = new itkSize3();
     itkSize3 gridBorderSize = new itkSize3();
     itkSize3 totalGridSize = new itkSize3();

     gridSizeOnImage.Fill(12);
     gridBorderSize.Fill(3);
     totalGridSize.Fill(15);

     bsplineRegion.SetSize(totalGridSize);

     itkVectorD3 spacing = fixedReader.GetOutput().GetSpacing();
     itkPointD3 origin = fixedReader.GetOutput().GetOrigin();
     itkSize3 fixedImageSize = fixedRegion.GetSize();

     for (int r = 0; r < 3; r++) {
       spacing.SetElement(r, spacing.GetElement(r) * Math.floor 
(((double) (fixedImageSize.GetElement(r) - 1)) / ((double)  
(gridSizeOnImage.GetElement(r) - 1))));
       origin.SetElement(r, origin.GetElement(r) - spacing.GetElement 
(r));
     }

     transform.SetGridSpacing(spacing);
     transform.SetGridOrigin(origin);
     transform.SetGridRegion(bsplineRegion);

     for (int i = 0; i < 3; i++) System.out.print(spacing.GetElement 
(i) + " ");
     System.out.println();
     for (int i = 0; i < 3; i++) System.out.print(origin.GetElement 
(i) + " ");
     System.out.println();
     for (int i = 0; i < 3; i++) System.out.print 
(bsplineRegion.GetSize(i) + " ");
     System.out.println();
     for (int i = 0; i < 3; i++) System.out.print 
(bsplineRegion.GetIndex(i) + " ");
     System.out.println();

     long numberOfParameters = transform.GetNumberOfParameters();

     itkArrayD parameters = new itkArrayD(numberOfParameters);
     parameters.Fill(0);
     transform.SetParameters(parameters);

     registration.SetInitialTransformParameters 
(transform.GetParameters());

     itkArrayI boundSelect = new itkArrayI 
(transform.GetNumberOfParameters());
     itkArrayD upperBound = new itkArrayD 
(transform.GetNumberOfParameters());
     itkArrayD lowerBound = new itkArrayD 
(transform.GetNumberOfParameters());
     boundSelect.Fill(0);
     upperBound.Fill(0.0);
     lowerBound.Fill(0.0);

     optimizer.SetBoundSelection(boundSelect);
     optimizer.SetUpperBound(upperBound);
     optimizer.SetLowerBound(lowerBound);
     optimizer.SetCostFunctionConvergenceFactor(1e7);
     optimizer.SetProjectedGradientTolerance(1e-4);
     optimizer.SetMaximumNumberOfIterations(500);
     optimizer.SetMaximumNumberOfEvaluations(500);
     optimizer.SetMaximumNumberOfCorrections(12);
     System.out.println(optimizer.GetBoundSelection 
().GetNumberOfElements() + " " + optimizer.GetBoundSelection 
().GetElement(0));

     metric.SetNumberOfHistogramBins(50);
     metric.SetNumberOfSpatialSamples((int)  
(fixedRegion.GetNumberOfPixels() * 0.1));

     class CommandIterationUpdate extends itkJavaCommand {
       public void Execute() {
         System.out.println("iteration " +  
optimizer.GetCurrentIteration() + " " + optimizer.GetValue() + " " +  
optimizer.GetInfinityNormOfProjectedGradient());
       }
     }

     CommandIterationUpdate p = new CommandIterationUpdate();
     registration.AddObserver(new itkIterationEvent(), p);

     registration.StartRegistration();

   }

   public static void main(String args[]) {
     try {
       defregister(args[0], args[1]);
     } catch (Exception e) {
       e.printStackTrace();
     }
   }
}