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<li>This is running on Windows 7 in a Release build (CMAKE_<span style="font-style: italic;">BUILD_</span>TYPE set to RelWithDebInfo)</li><li>I’m not sure how to use a system version of HDF5, would I need to re-build itk with HDF5 somehow left out?</li><li>It appears to be just this one file. The MHD follows, sharing the RAW would be trickier …</li></ol>
<div>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.</div>
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<div>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 …</div>
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<div>Thanks,</div>
<div>Chris</div>
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<div>MHD file looks like this:</div>
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<div>ObjectType = Image</div>
<div>NDims = 3</div>
<div>BinaryData = True</div>
<div>BinaryDataByteOrderMSB = False</div>
<div>CompressedData = False</div>
<div>TransformMatrix = 1 0 0 0 1 0 0 0 1</div>
<div>Offset = 0 0 0</div>
<div>CenterOfRotation = 0 0 0</div>
<div>AnatomicalOrientation = RAI</div>
<div>ElementSpacing = 0.615234 0.615234 0.5</div>
<div>DimSize = 512 512 540</div>
<div>ElementType = MET_SHORT</div>
<div>ElementDataFile = media-IO.20140509.1233344180.n540.recon.itks163d.raw</div>
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<span style="font-weight:bold">From: </span>Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
<span style="font-weight:bold">Date: </span>Friday, May 9, 2014 at 12:30 PM<br>
<span style="font-weight:bold">To: </span>Chris Cooper <<a href="mailto:chris.cooper@veranmedical.com">chris.cooper@veranmedical.com</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:community@itk.org">community@itk.org</a>" <<a href="mailto:community@itk.org">community@itk.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ITK] itk 4.5.1 crashing in HDF5<br>
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Hello,
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<div>What is you platform, architecture and are you using the ITK provided HDF5? How are you compiling ITK Debug Release?</div>
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<div>If you use a system version of HDF5 do you still get the issue?</div>
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<div>Is there an issue will all HDF5 files your just this one? Can you share the problematic file?</div>
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<div>Brad</div>
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<div>On May 9, 2014, at 2:23 PM, Chris Cooper <<a href="mailto:chris.cooper@veranmedical.com">chris.cooper@veranmedical.com</a>> wrote:</div>
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<div>While trying to read a file, we get a crash with this call stack:</div>
<div>H5MM_xfree</div>
<div>H5E_<span style="font-style: italic;">printf_</span>stack</div>
<div>H5E_<span style="font-style: italic;">clear_</span>stack</div>
<div>H5Fis_hdf5</div>
<div>H5::H5File::isHdf5</div>
<div>HDF5ImageIO::CanReadFile</div>
<div>ImageIOFactory::CreateImageIO</div>
<div>ImageFileReader<…>::GenerateOutputInformation</div>
<div>ProcessObject::UpdateOutputInformation</div>
<div>ImageBase<3>::UpdateOutputInformation</div>
<div>DataObject::Update</div>
<div>ProcessObject::Update</div>
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<div>The code that calls itk looks like this:</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>ReaderType::Pointer reader = ReaderType::New();</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"> reader->DebugOff();</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"> reader->SetGlobalWarningDisplay(<span style="color: #bb2ca2">false</span>);</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"> reader->SetFileName(cache.pathForUid(uid).string());</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"> reader->Update();</div>
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<div>This looks similar to an issue discussed here:</div>
<div><a href="http://www.itk.org/pipermail/insight-users/2013-November/049157.html">http://www.itk.org/pipermail/insight-users/2013-November/049157.html</a></div>
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<div>Any thoughts on this problem? Is there a chance it’s been solved in 4.5.2 (which I am downloading & building now)?</div>
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<div>Thanks,</div>
<div>Chris</div>
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