[Insight-developers] BillsBasement Nightly Failing Test
Luis Ibanez
luis.ibanez at kitware.com
Mon Feb 23 23:10:04 EST 2009
Hi Brad,
The changes have been committed.
Here is the log & diff
http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/IO/itkMetaImageIO.cxx?root=Insight&r1=1.93&r2=1.94&sortby=date
--------------------------------------------------------------------------------------------
BUG: When comparing the largestRegion against the m_ImageIORegion, the
minimum
of the dimensions of the two should be used. The reason is that it
should
possible to read a 2D image into a 3D image, (as a 1-slice 3D image)
and
it should be possible to read a 3D image into a 2D image by taking only
the first slice. If we don't use the min dimension between the
largestRegion
and the m_ImageIORegion, one of the two is going to try to access
elements
out of bound during their comparison of index components and sizes.
--------------------------------------------------------------------------------------------
It almost look like this comparison & assignment
should be part of the API of the ImageIORegion...
Luis
-------------------------------------------------------------------------------------------------------
On Mon, Feb 23, 2009 at 10:53 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
> Hi Brad,
>
> Thanks for looking at this.
>
> I think the problem is that this expression should be using the minimum of
> both dimensions
> between the largestRegion and the m_ImageIORegion.
>
>
> I have the following local diff, that seems to fix the problem.
> I'm running some more test before committing it.
>
>
>
> Index: itkMetaImageIO.cxx
> ===================================================================
> RCS file: /cvsroot/Insight/Insight/Code/IO/itkMetaImageIO.cxx,v
> retrieving revision 1.93
> diff -r1.93 itkMetaImageIO.cxx
> 832,833c832,836
> < // Pass the IO region to the MetaImage library
> < unsigned int nDims = this->GetNumberOfDimensions();
> ---
> > const unsigned int nDims = this->GetNumberOfDimensions();
> > const unsigned int ioDims = this->m_IORegion.GetImageDimension();
> >
> > const unsigned int minDimension = ( nDims > ioDims ) ? ioDims : nDims;
> >
> 837,838c840,841
> < ImageIORegion largestRegion(m_IORegion);
> < for(unsigned int i=0; i<nDims; i++)
> ---
> > ImageIORegion largestRegion(minDimension);
> > for(unsigned int i=0; i<minDimension; i++)
> 846,848c849,851
> < int* indexMin = new int[nDims];
> < int* indexMax = new int[nDims];
> < for(unsigned int i=0;i<nDims;i++)
> ---
> > int* indexMin = new int[minDimension];
> > int* indexMax = new int[minDimension];
> > for(unsigned int i=0;i<minDimension;i++)
> -------------------------------------------------------------
>
> Similar minDimension code has been used in
> itkImageIORegion.h in lines 299-308
>
>
>
> Luis
>
>
> --------------------------------------------------------
>
> On Mon, Feb 23, 2009 at 10:42 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> > wrote:
>
>> Hello,
>>
>> I am glad this was tracked down! Sorry it was my fault :(
>>
>> Giving it a quick look I see a small problem with this change:
>>
>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/IO/itkMetaImageIO.cxx?root=Insight&r1=1.92&r2=1.93
>>
>> nDim and the dimensionality of m_RegionIO may not match. Not sure why it'd
>> be failing since the 30th if this was the case. I'll have to give this some
>> more thought tomorrow. When those dimensions don't match is a tricky
>> case....
>>
>> Brad
>>
>> On Feb 23, 2009, at 10:04 PM, Luis Ibanez wrote:
>>
>> Hi Brad,
>>
>> This error seems to be related to the changes in MetaImage.
>>
>> Here is the backtrace that I get from GDB:
>>
>>
>> -----------------------------------------------------------------------
>>
>> (gdb) run itkImageToCooccurrenceListAdaptorTest
>> /home/ibanez/src/Insight/Testing/Data/Input/HeadMRVolume.mhd
>> Starting program:
>> /home/ibanez/bin/InsightGcc4.3/Debug/bin/itkStatisticsTests
>> itkImageToCooccurrenceListAdaptorTest
>> /home/ibanez/src/Insight/Testing/Data/Input/HeadMRVolume.mhd
>> [Thread debugging using libthread_db enabled]
>> /usr/include/c++/4.3/debug/vector:237:error: attempt to subscript
>> container
>> with out-of-bounds index 2, but container only holds 2 elements.
>>
>> Objects involved in the operation:
>> sequence "this" @ 0x0xbf9e58fc {
>> type = NSt7__debug6vectorIlSaIlEEE;
>> }
>> [New Thread 0xb7d0e6c0 (LWP 8686)]
>>
>> Program received signal SIGABRT, Aborted.
>> [Switching to Thread 0xb7d0e6c0 (LWP 8686)]
>> 0xb7fe4430 in __kernel_vsyscall ()
>> (gdb) bt
>> #0 0xb7fe4430 in __kernel_vsyscall ()
>> #1 0xb7d3b8a0 in raise () from /lib/tls/i686/cmov/libc.so.6
>> #2 0xb7d3d268 in abort () from /lib/tls/i686/cmov/libc.so.6
>> #3 0xb7ecd849 in __gnu_debug::_Error_formatter::_M_error () from
>> /usr/lib/libstdc++.so.6
>> #4 0x083c9d14 in std::__debug::vector<long, std::allocator<long>
>> >::operator[] (this=0xbf9e58fc, __n=2) at
>> /usr/include/c++/4.3/debug/vector:237
>> #5 0x083c9d53 in itk::ImageIORegion::SetIndex (this=0xbf9e58f4, i=2,
>> idx=0) at /home/ibanez/src/Insight/Code/IO/itkImageIORegion.h:183
>> #6 0x085a60b8 in itk::MetaImageIO::Read (this=0x9335f40,
>> buffer=0x93501a8) at /home/ibanez/src/Insight/Code/IO/itkMetaImageIO.cxx:840
>> #7 0x084a2efb in itk::ImageFileReader<itk::Image<float, 2u>,
>> itk::DefaultConvertPixelTraits<float> >::GenerateData (this=0x9331cf0) at
>> /home/ibanez/src/Insight/Code/IO/itkImageFileReader.txx:406
>> #8 0x0884cc49 in itk::ProcessObject::UpdateOutputData (this=0x9331cf0) at
>> /home/ibanez/src/Insight/Code/Common/itkProcessObject.cxx:991
>> #9 0x0883412b in itk::DataObject::UpdateOutputData (this=0x9334410) at
>> /home/ibanez/src/Insight/Code/Common/itkDataObject.cxx:420
>> #10 0x0883406a in itk::DataObject::Update (this=0x9334410) at
>> /home/ibanez/src/Insight/Code/Common/itkDataObject.cxx:344
>> #11 0x0884c00d in itk::ProcessObject::Update (this=0x9331cf0) at
>> /home/ibanez/src/Insight/Code/Common/itkProcessObject.cxx:619
>> #12 0x084855f3 in itkImageToCooccurrenceListAdaptorTest (argc=2,
>> argv=0xbf9e6008) at
>> /home/ibanez/src/Insight/Testing/Code/Numerics/Statistics/itkImageToCooccurrenceListAdaptorTest.cxx:53
>> #13 0x0838fe3d in main (ac=3, av=0xbf9e6004) at
>> /home/ibanez/src/Insight/Code/Common/itkTestMain.h:162
>> -----------------------------------------------------------------------
>>
>> For some reason the itkImageIORegion thinks it is a 2D one
>> while the MetaImage is asking for the component [2].
>>
>>
>> Bill:
>> I'm looking at the CVS diff of the day that you pointed out.
>>
>>
>>
>> Luis
>>
>>
>> -----------------------------------------------------------------------
>>
>> On Mon, Feb 23, 2009 at 7:34 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>>
>>> Hi Bill,
>>>
>>> I'm looking at it...
>>>
>>> building with gcc 4.3 and STL debug on...
>>>
>>> Luis
>>>
>>>
>>> ---------------------------
>>>
>>> Bill Lorensen wrote:
>>>
>>>> Luis,
>>>>
>>>> This build has stl debugging turned on. The test:
>>>> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=277757
>>>> shows an issue. Typically the culprit can be found by running the test
>>>> from this build with gdb. However, I'm out of town and don't have
>>>> access to my basement machine.
>>>>
>>>> I notice that other platforms are crashing also. The failures started
>>>> on Jan 30. Since this test uses a meta file, I would look at the
>>>> changes to MetaImageIO that occurred that day:
>>>>
>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/IO/itkMetaImageIO.cxx?root=Insight&r1=1.89&r2=1.90
>>>>
>>>>
>>>> Bill
>>>>
>>>>
>>
>>
>
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