[Insight-users] Segmentation fault when calling itk::KdTree::Search(queryPoint, radius, neighbors)

[motes motes]

[New Thread 0x7f14a7c5f750 (LWP 4955)]
[New Thread 0x7f14a4299950 (LWP 4958)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f14a4299950 (LWP 4958)]
itk::Statistics::KdTree<itk::Statistics::ListSample<itk::Vector<double,
3u> > >::NearestNeighborSearchLoop (this=0x1d0cf30, node=0x1d0e1f0,
query=@0x7f14a4298cf0,
    lowerBound=@0x7f14a4298ac0, upperBound=@0x7f14a4298aa0) at
/home/mort/local/InsightToolkit-3.14.0/Code/Numerics/Statistics/itkKdTree.h:448
448	        if ( m_Distances[i] > farthestDistance )
(gdb)






On Sun, Nov 29, 2009 at 10:27 AM, Karthik Krishnan
<karthik.krishnan at kitware.com> wrote:
> If you get a segfault, please post the stack trace using gdb.
>
> On Sat, Nov 28, 2009 at 5:47 AM, motes motes <mort.motes at gmail.com> wrote:
>> I use the following types to create a KdTree:
>>
>>  typedef Vector<TScalarType, SpaceDimension>
>>          VectorType;
>>  typedef itk::Statistics::ListSample<VectorType>
>>              SampleType;
>>  typedef itk::Statistics::KdTreeGenerator< SampleType >
>>        TreeGeneratorType;
>>  typedef typename TreeGeneratorType::KdTreeType
>>         TreeType;
>>  typedef typename TreeType::InstanceIdentifierVectorType
>>       NeighborsType;
>>
>>
>>  typename SampleType::Pointer sample  = SampleType::New();
>>  typename TreeGeneratorType::Pointer treeGenerator = TreeGeneratorType::New();;
>>  typename TreeType::Pointer tree;
>>
>>
>> I create the tree with:
>>
>>  this->sample->SetMeasurementVectorSize(Dimension);
>>  VectorType mv;
>>  for (unsigned int i = 0 ; i < 1000 ; ++i ) {
>>    mv[0] = (float) i;
>>    mv[1] = (float) ((1000 - i) / 2 );
>>    mv[2] = (float) ((1000 - i) / 2 );
>>    sample->PushBack( mv );
>>  }
>>
>>  treeGenerator->SetSample(sample);
>>  treeGenerator->SetBucketSize(16);
>>  treeGenerator->Update();
>>  tree = treeGenerator->GetOutput();
>>
>>
>>
>>
>> From the function"TransformPoint" (in a transform I have created) I
>> then call the Search method:
>>
>>  NeighborsType neighbors;
>>    VectorType vectorPoint;
>>    vectorPoint.Fill(0);
>>    for (int i=0; i<NDimensions; i++) {
>>      vectorPoint[i] = point[i];
>>    }
>>  tree->Search(vectorPoint, 10.0, neighbors);
>>
>>
>>
>>
>> But when I run the application I get a segmentation fault. I have
>> tried to run the application with Valgrind but I get no error:
>>
>> valgrind --leak-check=yes --track-origins=yes ./MyApp
>> INFO:: Computing registered image
>> ==8389==
>> ==8389== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8 from 1)
>> ==8389== malloc/free: in use at exit: 0 bytes in 0 blocks.
>> ==8389== malloc/free: 13,153,309 allocs, 13,153,309 frees,
>> 8,529,290,300 bytes allocated.
>> ==8389== For counts of detected errors, rerun with: -v
>> ==8389== All heap blocks were freed -- no leaks are possible.
>>
>>
>>
>> I am pretty sure that the problem is the dynamic array 'neighbors'. If
>> I call the version of Search where the number of neighbors are
>> specified I don't get any segmentation fault:
>>
>>
>>  NeighborsType neighbors;
>>    VectorType vectorPoint;
>>    vectorPoint.Fill(0);
>>    for (int i=0; i<NDimensions; i++) {
>>      vectorPoint[i] = point[i];
>>    }
>>  unsigned int numberOfNeighbors = 3;
>>  tree->Search( vectorPoint, numberOfNeighbors, neighbors ) ;
>>
>> But since I need the version where the radius is specified the above
>> is not an option.
>>
>>
>>
>> Another thing. The error only occurs when I run a resampling Filter.
>> If I run the transform through a registration process it works fine.
>> The resampling Filter is created like this:
>>
>> typedef itk::ResampleImageFilter< FixedImageType, FixedImageType >
>>                           ResampleFilterType;
>> typedef itk::LinearInterpolateImageFunction< FixedImageType, double >
>>                           LinearInterpolatorType;
>>
>>  LinearInterpolatorType::Pointer linearInterpolator =
>> LinearInterpolatorType::New();
>>  ResampleFilterType::Pointer resampler = ResampleFilterType::New();
>>  resampler->SetInput(imageM);
>>  resampler->SetTransform(adaptiveTransform);
>>  resampler->SetInterpolator(linearInterpolator);
>>  resampler->SetOutputOrigin(imageF->GetOrigin());
>>  resampler->SetOutputSpacing(imageF->GetSpacing());
>>  resampler->SetSize(imageF->GetLargestPossibleRegion().GetSize());
>>  resampler->SetDefaultPixelValue(0);
>>
>>
>>  try {
>>
>>    resampler->Update();
>>
>>  }
>>
>>  catch( itk::ExceptionObject & err ) {
>>
>>    std::cerr << "ExceptionObject caught !" << std::endl;
>>
>>    std::cerr << err << std::endl;
>>
>>  }
>>
>>
>> Any ideas are most welcome!
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