[Insight-users] Adaptive Thresholding segmentation fault

[Oleksandr Dzyubak]

Hi Kishore,

To make things easier, I used the image from your submission.

Alex

Kishore Mosaliganti wrote:
> Hi Alex,
>
> Thanks for the report. I did not update the filter. I downloaded and
> retested at my end on Fedora Core 11, and it worked fine.
>
> From your error messages, it seems that the following filter:
> BSplineScatteredDataPointSetToImageFilter (itk)
>
> is throwing an error. It is a new filter in the review directory.
>
> The above filter is used to smoothly interpolate the adaptive
> threshold function throughout the image. What are the spacing and
> origin of your images?
>
> I will investigate what is happening and get back to you.
>
>
> Kishore
>
> On Sun, Nov 8, 2009 at 12:38 PM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
>   
>> 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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>>>>>>             
>>>>         
>>