[Insight-users] Reading portion of image file

Thu Nov 14 11:22:18 EST 2013

Hi all,

I wonder if this problem has ever been solved/fixed.
I'm experiencing (what I think is) exactly the same weird bug when reading a large number of nifti images.

The first option in the code below (sampleRegion = true) produces the same message after approx. 200 images, the second one (= false) works fine... Instantiating a new reader in every loop also works.  

Running the current git version.

Cheers
Alex

for( unsigned int subject = 0; subject < numSubjects; ++subject )
{
  imageReader->SetFileName( filenames[subject].c_str() );
  imageReader->Update();

  if( sampleRegion )
  {
    IteratorType it( imageReader->GetOutput(), samplingRegion );
    for( it.GoToBegin(); !it.IsAtEnd(); ++it )
    {
      FeatureValueType value = it.Get(); // ...
    }
  }
  else
  {
    IteratorType it( imageReader->GetOutput(), imageReader->GetOutput()->GetRequestedRegion() );
    for( it.GoToBegin(); !it.IsAtEnd(); ++it )
    {
      FeatureValueType value = it.Get(); // ...
    }
  }
}

Am 08. März 2012 um 17:00 schrieb Bradley Lowekamp <blowekamp at mail.nih.gov>:

Hello Matthias,

You are correct that the documentation for the ImageFileReader::EnlargeOutputRequestedRegion should be updated. However only certain ImageIO file formats support the "stream" or roi reading. The one derived from the StreamingImageIO base along with nift, and maybe others support this functionality. You'd have to look at ImageIO to know for sure.

Your usage of the ImageFileReader->ExtactImageFilter was scenario to motivate for the recent optimization of making the Extract filter run InPlace. That is very nice usage!

It looks like you have encountered a bug. Most likely some one is not closing a file, and you are running out of file descriptors for the process.

Here is the procedure for reporting a bug:
http://www.itk.org/Wiki/ITK/Procedure_for_Contributing_Bug_Fixes

If you have a "working" bit of code which exhibits the bug, that would help us reproduce the issue and should be included. This will help expedite the solution. If you have a patch to fix it even better.

I am suspicious that the new HDF5 ImageIO is not closing the file in the CanRead method.

Brad

On Mar 8, 2012, at 10:31 AM, Matthias Schneider wrote:

Hi.

I'm trying to extract subregions of 2D image files. Ideally, I'd like to 
read the required data only.
In the ITK doc I came across the comment in
itk::ImageFileReader::EnlargeOutputRequestedRegion() saying that:
"ImageFileReader cannot currently read a portion of an image (since the 
ImageIO objects cannot read a portion of an image)"

I'm not quite sure if this still holds. After a quick experiment, I was 
pretty much confident that the readers are in fact able to read portions:

const std::string fname = "/path/to/my/image.nii"; // [2048x2048 px]
typedef itk::Image<Pixel8uType, 2> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;

ImageType::RegionType roi;
roi.SetSize(0, 512);
roi.SetSize(1, 512);

for (int i = 0; i < N; ++i) {
  std::cout << i << std::endl;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(fname);
  reader->GetOutput()->SetRequestedRegion(roi);
  reader->Update();
}

At first glance, this works perfectly fine (I checked the buffered data 
chunk) and runs much faster than reading the entire slice. Choosing N 
very large (say 1024), the program crashes since the reader seems to not 
close the file descriptors properly. I get the following error:

HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
  #000: [...]/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c line 
794 in H5Fis_hdf5(): unable to open file
    major: Low-level I/O
    minor: Unable to initialize object
  #001: [...]/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 
1086 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #002: [...]/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c 
line 348 in H5FD_sec2_open(): unable to open file: name = 
'/path/to/my/image.nii', errno = 24, error message = 'Too many open 
files', flags = 0, o_flags = 0
    major: File accessability
    minor: Unable to open file
terminate called after throwing an instance of 
'itk::ImageFileReaderException'
  what(): 
[...]/ITK/Modules/IO/ImageBase/include/itkImageFileReader.hxx:143:
 Could not create IO object for file /path/to/my/image.nii
The file couldn't be opened for reading.
Filename: /path/to/my/image.nii

I also tried to explicitly use the ExtractImageFilter:

[... same as above ...]
typedef itk::ExtractImageFilter<ImageType, ImageType> ExtractFilterType;

for (int i = 0; i < N; ++i) {
  std::cout << i << std::endl;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(fname);
  // reader->Update();

  ExtractFilterType::Pointer extractor =  ExtractFilterType::New();
  extractor->SetInput(reader->GetOutput());
  extractor->SetExtractionRegion(roi);
  extractor->InPlaceOn(true);
  extractor->Update();
}

Without the reader->Update() the program still crashes when choosing N 
sufficiently large (~1024). Updating the reader first of course reads 
the entire slice (what I really want to avoid).
So does this mean that the comment in the manual still holds and the 
ImageIO is not able to correctly handle this case even though the 
buffered data chunks are correctly imported?! This confuses me a bit or 
maybe I'm missing something else?!

I'm happy about any comments or suggestions.

Thanks,
Matthias
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========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov

_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.html

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