[Insight-developers] BillsBasement Nightly Failing Test
Luis Ibanez
luis.ibanez at kitware.com
Tue Feb 24 08:16:39 EST 2009
Brad,
mm,...
I don't see how...,
minIndex and maxIndex are populated with values taken from
m_IORegion.GetIndex()[i];
so, there is no way to use more elements that the ones
contained in m_IORegion...
I think we should add a formal test to IO for
- Reading a 2D image file into a 3D image type
- Reading a 3D image file into a 2D image type
This will illustrate both cases, and then we can verify if
the behavior is correct.
Luis
----------------------------------------------------------------------------------
On Mon, Feb 23, 2009 at 11:19 PM, Bradley Lowekamp
<blowekamp at mail.nih.gov>wrote:
> I think that indexMin and indexMax still need to be nDims size.?
> I agree that it make since to make this type of comparison part of the
> ImageIORegion API. As that is the only reason for this issue it to remove
> padded 1's at the end.
>
>
> On Feb 23, 2009, at 11:10 PM, Luis Ibanez wrote:
>
> 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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