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BUG: Removing open HDF5 files causes segmentation fault #5784

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Merged
hjmjohnson merged 1 commit into from
Feb 11, 2026
Merged

BUG: Removing open HDF5 files causes segmentation fault #5784

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250 changes: 127 additions & 123 deletions Modules/IO/HDF5/test/itkHDF5ImageIOStreamingReadWriteTest.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -91,145 +91,149 @@ template <typename TPixel>
int
HDF5ReadWriteTest2(const char * fileName)
{
// Define image type.
using ImageType = typename itk::Image<TPixel, 3>;

// Create a source object (in this case a constant image).
typename ImageType::SizeType size;
size[2] = 5;
size[1] = 5;
size[0] = 5;
const typename itk::DemoImageSource<ImageType>::Pointer imageSource = itk::DemoImageSource<ImageType>::New();
imageSource->SetValue(static_cast<TPixel>(23)); // Not used.
imageSource->SetSize(size);

// Write image with streaming.
using WriterType = typename itk::ImageFileWriter<ImageType>;
auto writer = WriterType::New();
using MonitorFilterType = typename itk::PipelineMonitorImageFilter<ImageType>;
auto writerMonitor = MonitorFilterType::New();
writerMonitor->SetInput(imageSource->GetOutput());
writer->SetFileName(fileName);
writer->SetInput(writerMonitor->GetOutput());
writer->SetNumberOfStreamDivisions(5);
try
{
writer->Write();
}
catch (const itk::ExceptionObject & err)
{
std::cout << "itkHDF5ImageIOTest" << std::endl << "Exception Object caught: " << std::endl << err << std::endl;
return EXIT_FAILURE;
}
{ // START an isolation block for the streaming readers and writers.
// For streaming to work, the itk::ImageFileReader / itk::ImageFileWriter
// pipeline and the itk::StreamingImageFilter will maintain handles to open HDF5 files
// until their destructors run.

// Check streaming regions.
if (!writerMonitor->VerifyInputFilterExecutedStreaming(5))
{
return EXIT_FAILURE;
}
typename ImageType::RegionType expectedRegion;
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 1);
typename MonitorFilterType::RegionVectorType writerRegionVector = writerMonitor->GetUpdatedBufferedRegions();
for (typename ImageType::RegionType::IndexValueType iRegion = 0; iRegion < 5; ++iRegion)
{
expectedRegion.SetIndex(2, iRegion);
if (writerRegionVector[iRegion] != expectedRegion)
using ImageType = typename itk::Image<TPixel, 3>;

// Create a source object (in this case a constant image).
typename ImageType::SizeType size;
size[2] = 5;
size[1] = 5;
size[0] = 5;
const typename itk::DemoImageSource<ImageType>::Pointer imageSource = itk::DemoImageSource<ImageType>::New();
imageSource->SetValue(static_cast<TPixel>(23)); // Not used.
imageSource->SetSize(size);

// Write image with streaming.
using WriterType = typename itk::ImageFileWriter<ImageType>;
auto writer = WriterType::New();
using MonitorFilterType = typename itk::PipelineMonitorImageFilter<ImageType>;
auto writerMonitor = MonitorFilterType::New();
writerMonitor->SetInput(imageSource->GetOutput());
writer->SetFileName(fileName);
writer->SetInput(writerMonitor->GetOutput());
writer->SetNumberOfStreamDivisions(5);
try
{
std::cout << "Written image region number " << iRegion << " :" << writerRegionVector[iRegion]
<< " doesn't match expected one: " << expectedRegion << std::endl;
writer->Write();
}
catch (const itk::ExceptionObject & err)
{
std::cout << "itkHDF5ImageIOTest" << std::endl << "Exception Object caught: " << std::endl << err << std::endl;
return EXIT_FAILURE;
}
}

// Force writer close.
writer = typename WriterType::Pointer();

// Read image with streaming.
using ReaderType = typename itk::ImageFileReader<ImageType>;
auto reader = ReaderType::New();
reader->SetFileName(fileName);
reader->SetUseStreaming(true);
auto readerMonitor = MonitorFilterType::New();
readerMonitor->SetInput(reader->GetOutput());
using StreamingFilter = typename itk::StreamingImageFilter<ImageType, ImageType>;
auto streamer = StreamingFilter::New();
streamer->SetInput(readerMonitor->GetOutput());
streamer->SetNumberOfStreamDivisions(5);
typename ImageType::Pointer image;
try
{
streamer->Update();
}
catch (const itk::ExceptionObject & err)
{
std::cout << "itkHDF5ImageIOTest" << std::endl << "Exception Object caught: " << std::endl << err << std::endl;
return EXIT_FAILURE;
}
image = streamer->GetOutput();

// Check the largest possible and buffered regions.
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetIndex(2, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 5);
if (image->GetLargestPossibleRegion() != expectedRegion)
{
std::cout << "Read image largest possible region: " << image->GetLargestPossibleRegion()
<< " doesn't match expected one: " << expectedRegion << std::endl;
}
if (image->GetBufferedRegion() != expectedRegion)
{
std::cout << "Read image buffered region: " << image->GetBufferedRegion()
<< " doesn't match expected one: " << expectedRegion << std::endl;
}

// Check image pixel values.
itk::ImageRegionIterator<ImageType> it(image, image->GetLargestPossibleRegion());
typename ImageType::IndexType idx;
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
idx = it.GetIndex();
const TPixel origValue(idx[2] * 100 + idx[1] * 10 + idx[0]);
if (itk::Math::NotAlmostEquals(it.Get(), origValue))
// Check streaming regions.
if (!writerMonitor->VerifyInputFilterExecutedStreaming(5))
{
std::cout << "Original Pixel (" << origValue << ") doesn't match read-in Pixel (" << it.Get() << ')' << std::endl;
return EXIT_FAILURE;
}
}
typename ImageType::RegionType expectedRegion;
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 1);
typename MonitorFilterType::RegionVectorType writerRegionVector = writerMonitor->GetUpdatedBufferedRegions();
for (typename ImageType::RegionType::IndexValueType iRegion = 0; iRegion < 5; ++iRegion)
{
expectedRegion.SetIndex(2, iRegion);
if (writerRegionVector[iRegion] != expectedRegion)
{
std::cout << "Written image region number " << iRegion << " :" << writerRegionVector[iRegion]
<< " doesn't match expected one: " << expectedRegion << std::endl;
return EXIT_FAILURE;
}
}

// Check number of streaming regions.
if (!readerMonitor->VerifyInputFilterExecutedStreaming(5))
{
return EXIT_FAILURE;
}
// Force writer close.
writer = typename WriterType::Pointer();

// Check streaming regions.
typename MonitorFilterType::RegionVectorType readerRegionVector = readerMonitor->GetUpdatedBufferedRegions();
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 1);
for (typename ImageType::RegionType::IndexValueType iRegion = 0; iRegion < 5; ++iRegion)
{
expectedRegion.SetIndex(2, iRegion);
if (readerRegionVector[iRegion] != expectedRegion)
// Read image with streaming.
using ReaderType = typename itk::ImageFileReader<ImageType>;
auto reader = ReaderType::New();
reader->SetFileName(fileName);
reader->SetUseStreaming(true);
auto readerMonitor = MonitorFilterType::New();
readerMonitor->SetInput(reader->GetOutput());
using StreamingFilter = typename itk::StreamingImageFilter<ImageType, ImageType>;
auto streamer = StreamingFilter::New();
streamer->SetInput(readerMonitor->GetOutput());
streamer->SetNumberOfStreamDivisions(5);
typename ImageType::Pointer image;
try
{
streamer->Update();
}
catch (const itk::ExceptionObject & err)
{
std::cout << "itkHDF5ImageIOTest" << std::endl << "Exception Object caught: " << std::endl << err << std::endl;
return EXIT_FAILURE;
}
image = streamer->GetOutput();

// Check the largest possible and buffered regions.
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetIndex(2, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 5);
if (image->GetLargestPossibleRegion() != expectedRegion)
{
std::cout << "Read image largest possible region: " << image->GetLargestPossibleRegion()
<< " doesn't match expected one: " << expectedRegion << std::endl;
}
if (image->GetBufferedRegion() != expectedRegion)
{
std::cout << "Read image region number " << iRegion << " :" << readerRegionVector[iRegion]
std::cout << "Read image buffered region: " << image->GetBufferedRegion()
<< " doesn't match expected one: " << expectedRegion << std::endl;
}

// Check image pixel values.
itk::ImageRegionIterator<ImageType> it(image, image->GetLargestPossibleRegion());
typename ImageType::IndexType idx;
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
idx = it.GetIndex();
const TPixel origValue(idx[2] * 100 + idx[1] * 10 + idx[0]);
if (itk::Math::NotAlmostEquals(it.Get(), origValue))
{
std::cout << "Original Pixel (" << origValue << ") doesn't match read-in Pixel (" << it.Get() << ')'
<< std::endl;
return EXIT_FAILURE;
}
}

// Check number of streaming regions.
if (!readerMonitor->VerifyInputFilterExecutedStreaming(5))
{
return EXIT_FAILURE;
}
}

// Check streaming regions.
typename MonitorFilterType::RegionVectorType readerRegionVector = readerMonitor->GetUpdatedBufferedRegions();
expectedRegion.SetIndex(0, 0);
expectedRegion.SetIndex(1, 0);
expectedRegion.SetSize(0, 5);
expectedRegion.SetSize(1, 5);
expectedRegion.SetSize(2, 1);
for (typename ImageType::RegionType::IndexValueType iRegion = 0; iRegion < 5; ++iRegion)
{
expectedRegion.SetIndex(2, iRegion);
if (readerRegionVector[iRegion] != expectedRegion)
{
std::cout << "Read image region number " << iRegion << " :" << readerRegionVector[iRegion]
<< " doesn't match expected one: " << expectedRegion << std::endl;
return EXIT_FAILURE;
}
}
} // END the streaming isolation block to force destructors and close files
// Clean working directory.
itk::IOTestHelper::Remove(fileName);

itk::IOTestHelper::Remove(fileName); // Must ensure that the file is closed before removing the file.
return EXIT_SUCCESS;
}

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