[Insight-users] crashes N-D Linear Time Exact Signed Euclidean Distance Transform
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Sun Jun 29 13:33:46 EDT 2008
Hi Alex,
I have reproduced your problem and I'm searching what is causing it
currently.
I'll let you know if I found the problem.
Regards,
Gaëtan
Le 19 juin 08 à 23:24, Oleksandr Dzyubak a écrit :
> Hi Gaëtan,
>
> Thanks for your help.
> I am still getting the error below.
>
> ******** Begin Error********
> dzyubak at debian: /Lehmann$ ./SignedMaurerDistanceMapImageFilterTest
> smallDataset.hdr out.hdr
> SignedMaurerDistanceMapImageFilterTest: /usr/local/include/
> InsightToolkit/Utilities/vxl/core/vnl/vnl_vector.h:168: T&
> vnl_vector<T>::operator()(unsigned int) [with T = double]: Assertion
> `i<size()' failed.
> Aborted
>
> *******End Error*******
>
> And I still want to make it work. In an attachment you can find the
> archived source tree dm.tar.gz
> which I downloaded from the link you provided.
> To the directory I also added the images I tried to work with.
> I am using Debian Etch with gcc "version 4.1.2 20061115 (prerelease)
> (Debian 4.1.1-21)",
> "cmake version 2.6-patch 0", and "Insight_CVS_Jun_03_2008.tar.gz".
>
> I would be more than happy if you could give me a hint on how to
> proceed.
>
> Alex
>
>
> Gaëtan Lehmann wrote:
>>
>> Hi,
>>
>> I'm afraid I can't reproduce any of the problems you have.
>> Can you send me your source tree? You seem to have put everything
>> in a “Lehmann” directory — maybe with it, I would be able to
>> reproduce them.
>>
>> Regards,
>>
>> Gaëtan
>>
>>
>>
>> Le 3 juin 08 à 21:36, Oleksandr Dzyubak a écrit :
>>
>>> Hi Gaëtan,
>>>
>>> Thanks for your help.
>>>
>>> I have rebuilt ITK to include all the changes made recently.
>>> Following the link you provided, I downloaded your version of the
>>> filter.
>>> During the compilation I got some warnings but was able to get an
>>> executable (see below).
>>> However when I ran the executable, the program crashed again
>>> with a different error message though (before it was malloc() from
>>> AnalyzeIO).
>>>
>>> **************** Begin Error Message *********
>>> dzyubak at debian: /Lehmann$ ./SignedMaurerDistanceMapImageFilterTest
>>> SquareBinary201.hdr test.hdr
>>> SignedMaurerDistanceMapImageFilterTest: /usr/local/include/
>>> InsightToolkit/Utilities/vxl/core/vnl/vnl_vector.h:168: T&
>>> vnl_vector<T>::operator()(unsigned int) [with T = double]:
>>> Assertion `i<size()' failed.
>>> Aborted
>>> ************** End Error Message ********
>>>
>>>
>>> *********** Begin Compilation Warnings ****
>>> dzyubak at debian: /BUILD$ make
>>> Scanning dependencies of target
>>> SignedMaurerDistanceMapImageFilterTest
>>> [100%] Building CXX object CMakeFiles/
>>> SignedMaurerDistanceMapImageFilterTest.dir/
>>> itkSignedMaurerDistanceMapImageFilterTest.cxx.o
>>> /home/dzyubak/Test/N-
>>> D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Lehmann/
>>> itkBinaryBorderImageFilter.txx: In member function 'void
>>> itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage
>>> >
>>> ::CompareLines
>>> (std::vector<itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage>::runLength,
>>> std::allocator<itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage>::runLength> >&, const
>>> std::vector<itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage>::runLength,
>>> std::allocator<itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage>::runLength> >&) [with TInputImage =
>>> itk::Image<double, 3u>, TOutputImage = itk::Image<double, 3u>]':
>>> /home/dzyubak/Test/N-
>>> D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Lehmann/
>>> itkBinaryBorderImageFilter.txx:250: instantiated from 'void
>>> itk::BinaryBorderImageFilter<TInputImage,
>>> TOutputImage>::ThreadedGenerateData(const typename
>>> TOutputImage::RegionType&, int) [with TInputImage =
>>> itk::Image<double, 3u>, TOutputImage = itk::Image<double, 3u>]'
>>> /home/dzyubak/Test/N-
>>> D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Lehmann/
>>> itkSignedMaurerDistanceMapImageFilterTest.cxx:69: instantiated
>>> from here
>>> /home/dzyubak/Test/N-
>>> D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Lehmann/
>>> itkBinaryBorderImageFilter.txx:405: warning: unused variable 'ee1'
>>> Linking CXX executable SignedMaurerDistanceMapImageFilterTest
>>> [100%] Built target SignedMaurerDistanceMapImageFilterTest
>>>
>>> ********* End Compilation Warnings *******
>>>
>>> Gaëtan Lehmann wrote:
>>>>
>>>> Hi,
>>>>
>>>> The SignedMaurerDistanceMapImageFilter won't work when the input
>>>> image is 2D but the filter is 3D — the size is 1 on one dimension.
>>>> I have fixed that in an external repository, with some other
>>>> changes to
>>>>
>>>> a. avoid spending so much time in the border detection
>>>> b. multithread it
>>>> c. make it work with any sizes on all the dimensions
>>>>
>>>> That work is available at
>>>>
>>>> http://voxel.jouy.inra.fr/darcs/contrib-itk/watershed
>>>>
>>>> You'll have to take the classes
>>>> SignedMaurerDistanceMapImageFilter and BinaryBorderImageFilter.
>>>>
>>>> I'll try to put b. and c. in ITK before the next release.
>>>> a. has to pass through the process of the peer review in the
>>>> insight journal before being integrated in ITK.
>>>>
>>>> Regards,
>>>>
>>>> Gaëtan
>>>>
>>>>
>>>> Le 2 juin 08 à 21:18, Oleksandr Dzyubak a écrit :
>>>>
>>>>> Hi Bill,
>>>>>
>>>>> Now I am a bit confused by what you are saying.
>>>>>
>>>>> 1) You say that it works for 3D but does not for 2D.
>>>>> I cannot understand that since 2D dimensionality is a particular
>>>>> case of 3D.
>>>>> Lets say 2D is a 3D with just one z-component. From my
>>>>> prospective, it has to work
>>>>> for 2D if it does for 3D. Opposite is not necessary true though.
>>>>>
>>>>> 2) If I comment the writer out, the program still crashes with
>>>>> the same error.
>>>>>
>>>>> 3) All my images are in the Analyze75 format
>>>>> and while using the other ITK filters I have not had any
>>>>> problems so far.
>>>>> (I mean with ITK Analyze reader/writer, except orientations, of
>>>>> course).
>>>>>
>>>>> Do you mean that even though my executables did not complain,
>>>>> the results I was getting could be wrong since I used ITK
>>>>> Analyze reader/writer?
>>>>>
>>>>> If so, in what fashion could the final results be wrong?
>>>>>
>>>>> Is it error-prone for some particular platform/compiler
>>>>> (Linux Debian with gcc 4.1.2 in my case) or it is more general
>>>>> case?
>>>>>
>>>>> How severe does it affect the final results?
>>>>>
>>>>> Thanks for your help,
>>>>>
>>>>> Alex
>>>>>
>>>>>
>>>>> Bill Lorensen wrote:
>>>>>> Oleksandr,
>>>>>>
>>>>>> There are some known problems in the ITK Analyze reader/writer
>>>>>> when
>>>>>> the images are 2D and not 3D. I think the read part has been
>>>>>> fixed
>>>>>> recently. However, the write part still has problems. If your
>>>>>> images
>>>>>> are 3D, then all should be fine. Until we fix this 2D Analyze
>>>>>> image
>>>>>> problem, I'm afraid you cannot run the filters.
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>> On Sun, Jun 1, 2008 at 1:07 PM, Oleksandr Dzyubak <adzyubak at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Hi Bill,
>>>>>>>
>>>>>>> This time I try to be more accurate.
>>>>>>>
>>>>>>> 1) I downloaded ITK from CVS, compiled with the RelWithDeb
>>>>>>> flag, and
>>>>>>> installed on my Linux box.
>>>>>>> 2) I have Debian Etch with gcc 4.1.2
>>>>>>> 3) The example itkSignedMaurerDistanceMapImageFilterTest.cxx
>>>>>>> was taken
>>>>>>> from ITK distro and not from IJ.
>>>>>>>
>>>>>>> Insight/Testing/Code/BasicFilters/
>>>>>>> itkSignedMaurerDistanceMapImageFilterTest.cxx
>>>>>>>
>>>>>>> 4) Example was compiled in debug mode.
>>>>>>> 5) As you advised, the example was run on both
>>>>>>> SquareBinary201.png and
>>>>>>> SquareBinary201.hdr.
>>>>>>>
>>>>>>> Results.
>>>>>>> As you predicted, the example has processed the *.png image
>>>>>>> taken from ITK
>>>>>>> distro resulting
>>>>>>> in a nice looking map.
>>>>>>>
>>>>>>> dzyubak at debian: /BUILD$ ./SignedMaurerDistanceMapImageFilterTest
>>>>>>> SquareBinary201.png test_png.hdr
>>>>>>> WARNING: In /root/Insight/Code/IO/itkAnalyzeImageIO.cxx, line
>>>>>>> 1280
>>>>>>> AnalyzeImageIO (0x8169a98): ERROR: Analyze 7.5 File Format
>>>>>>> Only Allows RPI,
>>>>>>> PIR, and RIP Orientation
>>>>>>>
>>>>>>> However when I tried to run it on a real stuff (all my images
>>>>>>> in Analyze75
>>>>>>> format), the same image but
>>>>>>> taken from IJ archive (SquareBinary201.hdr), it crashes.
>>>>>
>>>>> _______________________________________________
>>>>> Insight-users mailing list
>>>>> Insight-users at itk.org
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>>> --Gaëtan Lehmann
>>>> Biologie du Développement et de la Reproduction
>>>> INRA de Jouy-en-Josas (France)
>>>> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
>>>> http://voxel.jouy.inra.fr http://www.mandriva.org
>>>> http://www.itk.org http://www.clavier-dvorak.org
>>>>
>>>
>>
>> --Gaëtan Lehmann
>> Biologie du Développement et de la Reproduction
>> INRA de Jouy-en-Josas (France)
>> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
>> http://voxel.jouy.inra.fr http://www.mandriva.org
>> http://www.itk.org http://www.clavier-dvorak.org
>>
>
> <dm.tar.gz>
--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.mandriva.org
http://www.itk.org http://www.clavier-dvorak.org
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