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

[Karthik Krishnan]

sumit shah wrote:

> Dear Itk Users:
>
> I was wondering if anyone has any thoughts or hints on this issue I 
> have stumbled upon. Thanks for your time in reading this!
>
> Thanks,
> Sumit
>
> On Sep 13, 2005, at 12:03 AM, sumit shah wrote:
>
>> 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
>>
The C++ version did not run for any iterations either. Set the dimension 
to 2 and it will.

Do you have a log of the transforms after each iteration ? What you 
would see is that the transform deviates too far from Identity and until 
there is hardly any overlap between the fixed and the moving image to 
compute a similarity metric. At this stage you would want to tweak the 
paramters.

HTH
karthik

>>
>> 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.itkImageRegistrationMetho 
>> dF3F3_Pointer_StartRegistration(Native Method)
>> at 
>> InsightToolkit.itkImageRegistrationMethodF3F3_Pointer.StartRegistratio 
>> n(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_Pointe 
>> r;
>> 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.itkLinearInterpolateImageFunction 
>> F3D_New();
>> final itkMattesMutualInformationImageToImageMetricF3F3_Pointer metric 
>> = 
>> itkMattesMutualInformationImageToImageMetricF3F3.itkMattesMutualInform 
>> ationImageToImageMetricF3F3_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();
>> }
>> }
>> }
>>
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>
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