[Insight-users] Adaptive Thresholding segmentation fault

[Oleksandr Dzyubak]

Hi Kishore,

I just have a chance to start over and test your program once again.
This time I am doing that on my laptop I386 32 bit 2GB.

dzyubak at debian-alex: /Img_Org$ uname -a
Linux debian-alex 2.6.26-2-686 #1 SMP Wed Nov 4 20:45:37 UTC 2009 i686 
GNU/Linux

dzyubak at debian-alex: /Img_Org$ gcc -v
gcc version 4.3.2 (Debian 4.3.2-1.1)

ITK-3.16

I just downloaded your submission from IJ and recompiled everything from 
scratch.
The input image and parameters are taken from your submission.

dzyubak at debian-alex: /Img_Org$ ls
adaptiveOtsuThresh2D  adaptiveOtsuThresh3D  input.png

Below are the results I am getting even for your 2D image.

dzyubak at debian-alex: /Img_Org$ time ./adaptiveOtsuThresh2D input.png 
output.png 20 5000 3 30
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  
/usr/local/include/InsightToolkit/Review/itkBSplineScatteredDataPointSetToImageFilter.txx:902:
itk::ERROR: PointSetToImageFilter(0x9161460): The collapse point 
component 108 is outside the corresponding parametric domain of [0, 108].
Aborted

real    0m1.804s
user    0m1.736s
sys    0m0.024s


Regards,

Alex

BTW.
On my server at work, at least 2D version worked.
Only the 3D version crashed.
Did you changed/updated your submission?


Kishore Mosaliganti wrote:
> Hi Alex,
>
> I tried out my large 3D datasets and I did not have any problem at my end.
>
> Can you make sure your data is being read correctly. You can put some
> writers to write it out. What about the image size, origin and
> spacing?
>
> Can you crop your dataset to a point where the bug is being replicated
> and then share that data?
>
> Thanks,
> Kishore
>
> On Thu, Nov 5, 2009 at 6:00 PM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
>   
>> Hi Kishore,
>>
>> Thanks for such quick response.
>> More specific?
>>
>> ITK-3.16
>> AMD64
>>
>> dzyubak at helium: /Tmp$ gcc -v
>> Using built-in specs.
>> Target: x86_64-linux-gnu
>> Configured with: ../src/configure -v --with-pkgversion='Debian 4.3.2-1.1'
>> --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs
>> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared
>> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
>> --enable-threads=posix --enable-nls
>> --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3
>> --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr
>> --enable-cld --enable-checking=release --build=x86_64-linux-gnu
>> --host=x86_64-linux-gnu --target=x86_64-linux-gnu
>> Thread model: posix
>> gcc version 4.3.2 (Debian 4.3.2-1.1)
>>
>>
>> dzyubak at helium: /Tmp$ uname -a
>> Linux helium 2.6.26-2-amd64 #1 SMP Mon Oct 19 02:34:17 UTC 2009 x86_64
>> GNU/Linux
>>
>> dzyubak at helium: /Tmp$ ls
>> adaptiveOtsuThresh3D  space_1mm_h61_with_psf.hdr  uchar_1mm_h61_with_psf.hdr
>> space_1mm_h61_with_psf.img  uchar_1mm_h61_with_psf.img
>>
>>
>> dzyubak at helium: /Tmp$ ./adaptiveOtsuThresh3D
>> Usage:
>> ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples
>> numOfLevels numOfControlPts
>>
>>
>> dzyubak at helium: /Tmp$ time ./adaptiveOtsuThresh3D uchar_1mm_h61_with_psf.hdr
>> uchar_1mm_h61_with_psf_segm_5_5000_3_30.hdr 5 5000 3 30
>> Segmentation fault
>>
>> real    1m1.959s
>> user    0m56.996s
>> sys    0m4.800s
>>
>>
>> Hope it helps,
>>
>> Alex
>>
>>
>> Kishore Mosaliganti wrote:
>>     
>>> Hi Alex,
>>>
>>> I made that submission and I use it almost everyday in my work. Can
>>> you be more specific on your problem. Whats the s
>>>
>>> On Thu, Nov 5, 2009 at 5:19 PM, Oleksandr Dzyubak <adzyubak at gmail.com>
>>> wrote:
>>>
>>>       
>>>> Hi guys,
>>>>
>>>> I just downloaded the filter from the submission:
>>>> http://hdl.handle.net/10380/3133
>>>> An Adaptive Thresholding Image Filter by Mosaliganti K., Gelas A.,
>>>> Megason
>>>> S.
>>>> and gave it a try.
>>>>
>>>> The 2D version works as described in the "howto" but
>>>> the 3D one gives the "Segmentation fault" error with core dumped.
>>>>
>>>> Did anybody try it for 3D images?
>>>>
>>>> Alex
>>>>
>>>>
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>>>>         
>>