[Insight-users] crashes N-D Linear Time Exact Signed Euclidean Distance Transform
Oleksandr Dzyubak
adzyubak at gmail.com
Fri May 30 10:43:05 EDT 2008
Yes, you are right.
I am using an installed ITK version (Insight_CVS_Apr_27_2008.tar.gz)
and N-D Linear Time Exact Signed Euclidean Distance Transform from IJ.
http://insight-journal.org/midas/handle.php?handle=1926/171
All the images and test programs are taken from that archive.
Bill Lorensen wrote:
> You are not getting a line # in itkAnalyzeImageIO.cxx. Looks like you
> are building against an installed ITK. Can you try to build your own
> version of ITK? The installed versionj does not have debug symbols.
> Also, where did you get SquareBinary201.hdr? We distribute a
> SquareBinary201.png.
>
> Bill
>
> On Fri, May 30, 2008 at 10:01 AM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
>
>> Hi Bill,
>>
>> I also was thinking of rebuilding ITK in the debug mode.
>> So last night I found a box and did that.
>> After running the valgrind on an executable, I got the lines causing failure
>> (from up to bottom).
>>
>> Actually, the program that causes failure is
>> "SignedMaurerDistanceMapImageFilterTest.cxx"
>> and in particular line 23 ( reader->Update(); actually generated by
>> (itkImageFileReader.txx:153) )
>> and line 38 ( writer->Update(); generated by (itkImageFileWriter.txx:232)
>> ). See log below.
>>
>> What could cause such a failure?
>>
>> Alex
>>
>> ********* Debug error log *******
>>
>> dzyubak at debian: /Images$ valgrind ./SignedMaurerDistanceMapImageFilterTest
>> SquareBinary201.hdr test.hdr
>>
>> ==5109== Invalid write of size 8
>> ==5109== at 0x40AE720: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109== Address 0x4f4f340 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x40AE5BE: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109==
>> ==5109== Invalid write of size 8
>> ==5109== at 0x40AE740: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109== Address 0x4f4f380 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x40AE638: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109==
>> ==5109== Invalid write of size 8
>> ==5109== at 0x40AE75A: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109== Address 0x4f4f3c0 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x40AE6B2: itk::AnalyzeImageIO::ReadImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
>> (itkImageFileReader.txx:153)
>> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
>> (itkImageBase.txx:177)
>> ==5109== by 0x44A9991: itk::DataObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
>> /usr/lib/libITKCommon.so.3.4.0)
>> ==5109== by 0x808C088: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
>> ==5109==
>> ==5109== Invalid read of size 8
>> ==5109== at 0x409D27E:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109== Address 0x5241e50 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x409D150:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109==
>> ==5109== Invalid read of size 8
>> ==5109== at 0x409D292:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109== Address 0x5241cd0 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x409D03D:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109==
>> ==5109== Invalid read of size 8
>> ==5109== at 0x409D2A6:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109== Address 0x5241b50 is 0 bytes after a block of size 16 alloc'd
>> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
>> ==5109== by 0x409CF30:
>> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
>> /usr/lib/libITKIO.so.3.4.0)
>> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::GenerateData() (itkImageFileWriter.txx:279)
>>>
>> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Write() (itkImageFileWriter.txx:232)
>>>
>> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>
>>> ::Update() (itkImageFileWriter.h:148)
>>>
>> ==5109== by 0x808C1D2: main
>> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
>> ==5109==
>> ==5109== ERROR SUMMARY: 6 errors from 6 contexts (suppressed: 71 from 1)
>> ==5109== malloc/free: in use at exit: 0 bytes in 0 blocks.
>> ==5109== malloc/free: 16,858 allocs, 16,858 frees, 3,500,876 bytes
>> allocated.
>> ==5109== For counts of detected errors, rerun with: -v
>> ==5109== All heap blocks were freed -- no leaks are possible.
>>
>> ************ End of log ******
>>
>> Bill Lorensen wrote:
>>
>>> Oleksandr,
>>>
>>> That's not a good error and may explain your problem. An invalid write
>>> means that it is trying to write to memory that is not allocated.
>>>
>>> You must be building release. If you build debug, valgrind will give
>>> the exact offending line.
>>>
>>> Bill
>>>
>>> On Thu, May 29, 2008 at 5:42 PM, Oleksandr Dzyubak <adzyubak at gmail.com>
>>> wrote:
>>>
>>>
>>>> Hi Bill,
>>>>
>>>> I ran valgrind on my box.
>>>>
>>>> dzyubak at debian: /Images$ valgrind --tool=memcheck
>>>> ./SignedMaurerDistanceMapImageFilterTest SquareBinary201.hdr test.hdr
>>>>
>>>> I got several interesting results.
>>>>
>>>> 1) Running valgrind on an executable results in producing output image
>>>> which
>>>> matches that
>>>> in the archive. This never happens if I just run an executable since a
>>>> program aborts right away.
>>>>
>>>> 2) Valgrind produces a huge log with errors. In the end it says:
>>>>
>>>> ==15656== ERROR SUMMARY: 29 errors from 7 contexts (suppressed: 69 from
>>>> 1).
>>>>
>>>> 3) And it starts its log with as below.
>>>>
>>>> ==15656== Invalid write of size 8
>>>> ==15656== at 0x40DF148: itk::AnalyzeImageIO::ReadImageInformation()
>>>> (in
>>>> /usr/local/lib/InsightToolkit/libITKIO.so.3.7.0)
>>>> ==15656== by 0x80C66A6: itk::ImageFileReader<itk::Image<int, 2>,
>>>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation() (in
>>>>
>>>> /home/dzyubak/Test/N-D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Images/SignedMaurerDistanceMapImageFilterTest)
>>>>
>>>>
>>>> Is this memory block size mismatch coming from type traits or what?
>>>> Any ideas how to treat that?
>>>>
>>>> Thanks,
>>>> Alex
>>>>
>>>>
>>>> Bill Lorensen wrote:
>>>>
>>>>
>>>>> Oleksandr,
>>>>>
>>>>> If you have valgrind on your linux box, try running it. It can find
>>>>> some tricky memory problems.
>>>>>
>>>>> Bill
>>>>>
>>>>>
>>>>
>>
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