[Insight-users] crashes N-D Linear Time Exact Signed Euclidean Distance Transform
Oleksandr Dzyubak
adzyubak at gmail.com
Mon Jun 30 11:18:12 EDT 2008
Hi Gaëtan,
Please let me know if any progress.
Thanks for your help,
Alex
Gaëtan Lehmann wrote:
>
> 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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