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Adaptive Thresholding segmentation fault
by Oleksandr
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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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Kishore Mosaliganti
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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@...> 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 > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.html > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Oleksandr
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Hi Kishore,
Thanks for such quick response. More specific? ITK-3.16 AMD64 dzyubak@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@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@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@helium: /Tmp$ ./adaptiveOtsuThresh3D Usage: ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples numOfLevels numOfControlPts dzyubak@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@...> 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 >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.html >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://www.itk.org/mailman/listinfo/insight-users >> >> _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Kishore Mosaliganti
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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@...> wrote: > Hi Kishore, > > Thanks for such quick response. > More specific? > > ITK-3.16 > AMD64 > > dzyubak@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@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@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@helium: /Tmp$ ./adaptiveOtsuThresh3D > Usage: > ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples > numOfLevels numOfControlPts > > > dzyubak@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@...> >> 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 >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.html >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users >>> >>> > > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Oleksandr
::
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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@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@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@debian-alex: /Img_Org$ ls adaptiveOtsuThresh2D adaptiveOtsuThresh3D input.png Below are the results I am getting even for your 2D image. dzyubak@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@...> wrote: > >> Hi Kishore, >> >> Thanks for such quick response. >> More specific? >> >> ITK-3.16 >> AMD64 >> >> dzyubak@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@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@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@helium: /Tmp$ ./adaptiveOtsuThresh3D >> Usage: >> ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples >> numOfLevels numOfControlPts >> >> >> dzyubak@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@...> >>> 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 >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.html >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.itk.org/mailman/listinfo/insight-users >>>> >>>> >>>> >> _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Kishore Mosaliganti
::
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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. $gcc -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.1 20090725 (Red Hat 4.4.1-2) (GCC) From your error messages, it seems that the following filter: BSplineScatteredDataPointSetToImageFilter (itk) is throwing an error. It is a new filter in the review directory. The above filter is used to smoothly interpolate the adaptive threshold function throughout the image. What are the spacing and origin of your images? I will investigate what is happening and get back to you. Kishore On Sun, Nov 8, 2009 at 12:38 PM, Oleksandr Dzyubak <adzyubak@...> wrote: > Hi Kishore, > > I just have a chance to start over and test your program once again. > This time I am doing that on my laptop I386 32 bit 2GB. > > dzyubak@debian-alex: /Img_Org$ uname -a > Linux debian-alex 2.6.26-2-686 #1 SMP Wed Nov 4 20:45:37 UTC 2009 i686 > GNU/Linux > > dzyubak@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@debian-alex: /Img_Org$ ls > adaptiveOtsuThresh2D adaptiveOtsuThresh3D input.png > > Below are the results I am getting even for your 2D image. > > dzyubak@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@...> >> wrote: >> >>> >>> Hi Kishore, >>> >>> Thanks for such quick response. >>> More specific? >>> >>> ITK-3.16 >>> AMD64 >>> >>> dzyubak@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@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@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@helium: /Tmp$ ./adaptiveOtsuThresh3D >>> Usage: >>> ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples >>> numOfLevels numOfControlPts >>> >>> >>> dzyubak@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@...> >>>> 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 >>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.html >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://www.itk.org/mailman/listinfo/insight-users >>>>> >>>>> >>>>> >>> >>> > > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Adaptive Thresholding segmentation fault
by Oleksandr
::
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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@...> 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@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@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@debian-alex: /Img_Org$ ls >> adaptiveOtsuThresh2D adaptiveOtsuThresh3D input.png >> >> Below are the results I am getting even for your 2D image. >> >> dzyubak@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@...> >>> wrote: >>> >>> >>>> Hi Kishore, >>>> >>>> Thanks for such quick response. >>>> More specific? >>>> >>>> ITK-3.16 >>>> AMD64 >>>> >>>> dzyubak@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@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@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@helium: /Tmp$ ./adaptiveOtsuThresh3D >>>> Usage: >>>> ./adaptiveOtsuThresh3D InputImage OutputImage radius numOfSamples >>>> numOfLevels numOfControlPts >>>> >>>> >>>> dzyubak@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@...> >>>>> 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 >>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.html >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://www.itk.org/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>>> >>>>>> >>>> >> _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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