[ITK] itk 4.5.1 crashing in HDF5

[Chris Cooper]

  1.  This is running on Windows 7 in a Release build (CMAKE_BUILD_TYPE  set to RelWithDebInfo)
  2.  I’m not sure how to use a system version of HDF5, would I need to re-build itk with HDF5 somehow left out?
  3.  It appears to be just this one file.  The MHD follows, sharing the RAW would be trickier …

Here’s a strange thing I just noticed.  Sometimes the program runs fine, in those cases I am getting an error "Not a TIFF file, bad magic number 25167 (0x624f).” - it’s when I don’t get that error that I get the crash instead.

We are doing some testing that makes it seem like dcmtk is the problem, if we use the official 3.6.0 release instead of the snapshot from last November, the problem goes away …

Thanks,
Chris

MHD file looks like this:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = 0 0 0
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 0.615234 0.615234 0.5
DimSize = 512 512 540
ElementType = MET_SHORT
ElementDataFile = media-IO.20140509.1233344180.n540.recon.itks163d.raw


From: Bradley Lowekamp <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Date: Friday, May 9, 2014 at 12:30 PM
To: Chris Cooper <chris.cooper at veranmedical.com<mailto:chris.cooper at veranmedical.com>>
Cc: "community at itk.org<mailto:community at itk.org>" <community at itk.org<mailto:community at itk.org>>
Subject: Re: [ITK] itk 4.5.1 crashing in HDF5

Hello,

What is you platform, architecture and are you using the ITK provided HDF5? How are you compiling ITK Debug Release?

If you use a system version of HDF5 do you still get the issue?

Is there an issue will all HDF5 files your just this one? Can you share the problematic file?

Brad


On May 9, 2014, at 2:23 PM, Chris Cooper <chris.cooper at veranmedical.com<mailto:chris.cooper at veranmedical.com>> wrote:

While trying to read a file, we get a crash with this call stack:
H5MM_xfree
H5E_printf_stack
H5E_clear_stack
H5Fis_hdf5
H5::H5File::isHdf5
HDF5ImageIO::CanReadFile
ImageIOFactory::CreateImageIO
ImageFileReader<…>::GenerateOutputInformation
ProcessObject::UpdateOutputInformation
ImageBase<3>::UpdateOutputInformation
DataObject::Update
ProcessObject::Update

The code that calls itk looks like this:
ReaderType::Pointer reader = ReaderType::New();
        reader->DebugOff();
        reader->SetGlobalWarningDisplay(false);
        reader->SetFileName(cache.pathForUid(uid).string());
        reader->Update();

This looks similar to an issue discussed here:
http://www.itk.org/pipermail/insight-users/2013-November/049157.html

Any thoughts on this problem?  Is there a chance it’s been solved in 4.5.2 (which I am downloading & building now)?

Thanks,
Chris

_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/cgi-bin/mailman/listinfo/community

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20140509/d7403a63/attachment-0002.html>