[Insight-developers] BillsBasement Nightly Failing Test
Bradley Lowekamp
blowekamp at mail.nih.gov
Tue Feb 24 09:55:53 EST 2009
Luis,
I agree we should add more tests. I thought I added enough IO tests :)
Should this just be for meta or test it with a bunch of types? I can't
think of a way to validate this except valgrind and std lib debug.
Based on this methods:
/** Dimension of the region to be written. This differs from the
* the image dimension and is calculated at run-time by examining
* the size of the image in each coordinate direction. */
unsigned int ImageIORegion::GetRegionDimension() const
I think we should add:
/* Performs element by element comparison up to the GetRegionDimension()
* This is equivalent to removing any trailing ones, then doing a
operator==
*/
bool ImageIORegion::IsEqualWithRegionDimension(const Self &) const
There are clear use cases for this for reading. But there is also
similar code for writing, is this need? In itkImageFileWriter there is
a check to make sure the paste region is inside the largest. This is
enforce the IORegions are the same image dimension. So it may not be,
but if we have IsEqualWithRegionDimension is east todo.
minIndex and maxIndex need to be padded with 1 up to nDims. This is
because metaIO has been initialized with nDims and is expecting things
to be of that size!
Brad
On Feb 24, 2009, at 8:16 AM, Luis Ibanez wrote:
>
> 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
>>>
>>>
>>
>>
>>
>
>
========================================================
Bradley Lowekamp
Lockheed Martin Contractor for
Office of High Performance Computing and Communications
National Library of Medicine
blowekamp at mail.nih.gov
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