Re: [GoFigure2-developers] Gofigure2 RELEASE : segmentaionn fault on image opening

[Arnaud GELAS]

Hi Antonin,

Can you give us a link where we could get this image to test, please?

Thanks,
Arnaud

On 03/21/2011 02:01 PM, antonin perrot-audet wrote:
> Hello Arnaud,
>
> I let some water flow under the bridges, I now have a working
> segmentation pipeline, for nucleis, taking a big image as an input,
> cutting it in many subregions, which are segmented, labeled and reassembled.
> I wanted to build Gofigure2 to see where you guys are at etc...
> I used VTK with all necessary options (Mysql...), ITK as well, both
> built in RELEASE.
> I compiled Gofigure2 without examples etc... and it *still has a
> segmentation fault and crashes on image loading* (any image). My ubuntu
> is clean, I mean out of the box clean, and I just downloaded the
> necessary libs etc...
>
> It seems like the debug version or releasewithdebuginfo version works
> though.... weird !
>
> Antonin

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[antonin Perrot-Audet]

Yes indeed, here is a link to the image :

http://fex.insa-lyon.fr/get?k=2Wo2jHU59yyZj9FI8YH

[Nicolas Rannou]

Hi Antonin,

That is weird indeed...

I successfully opened the image on my Ubuntu 10.10 (amd64) in
release-shared.
Kishore was able to open it in release-static as well...

Which version of gofigure2 are you using? We recommend to use the master
branch of our git repository:
git clone g...@github.com:gofigure2/GoFigure2.git gofigure2

Could you tell us more about your configuration:
version of Ubuntu?
version of ITK?
version of VTK?
version of Boost? (provided by Ubuntu or compiled by yourself?)
version of MySQL? (provided by Ubuntu or compiled by yourself?)
version of Qt? (provided by Ubuntu or compiled by yourself?)
version of GoFigure2?

Did you give a try to the superbuild?
You can turn it on in cmake: it should download and compile all the
required libraries for you!

Thanks

Nicolas

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[Arnaud GELAS]

On 03/21/2011 04:11 PM, Nicolas Rannou wrote:
> Hi Antonin,
>
> That is weird indeed...
>
> I successfully opened the image on my Ubuntu 10.10 (amd64) in
> release-shared.
> Kishore was able to open it in release-static as well...
>
> Which version of gofigure2 are you using? We recommend to use the master
> branch of our git repository:
> git clone g...@github.com:gofigure2/GoFigure2.git gofigure2
>
> Could you tell us more about your configuration:
> version of Ubuntu?
> version of ITK?
> version of VTK?
> version of Boost? (provided by Ubuntu or compiled by yourself?)
> version of MySQL? (provided by Ubuntu or compiled by yourself?)
> version of Qt? (provided by Ubuntu or compiled by yourself?)
> version of GoFigure2?
>
> Did you give a try to the superbuild?

(Note that the superbuild feature is accessible on the develop branch,
so it would be better at first to stick on the master branch)

[Antonin Perrot-Audet]

Yep I used the master branch for compilation.
Please tell me which type of report about my system do you expect ?
Do you want me to send you my CMakeCache for GoFigure, ITK and VTK ?
do you hav any idea of a usefull tool for such system configuration report ?

--
Antonin Perrot-Audet
Electrical Engineering& Computer Sciences, INSA Lyon
M2 GEGP Signal& Image Processing, INSA Lyon, UCBL, Centrale Lyon

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[antonin perrot-audet]

Here are the CMakeCahce files for ITK, VTK, and GOFIGURE.
some version control :
mysql --version
mysql Ver 14.14 Distrib 5.1.49, for debian-linux-gnu (x86_64) using
readline 6.1

qmake --version
QMake version 2.01a
Using Qt version 4.7.0 in /usr/lib

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[antonin perrot-audet]

Here are the CMakeCahce files for ITK, VTK, and GOFIGURE.
some version control :
mysql --version
mysql Ver 14.14 Distrib 5.1.49, for debian-linux-gnu (x86_64) using
readline 6.1

qmake --version
QMake version 2.01a
Using Qt version 4.7.0 in /usr/lib

On 03/21/2011 09:15 PM, Arnaud GELAS wrote:

[Arnaud GELAS]

Antonin,

Thanks for all this information, we will investigate it!!!

Can you tell us which version of itk, vtk and gofigure you were using,
please?

If it is the git version, could you provide the hash of the last commit
by running git log, please?
Else just provide the release version.

Thanks,
Arnaud

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[antonin perrot-audet]

Hello,
the versions I use :

for VTK : (git version)
9d213da0f0fc55ed74e3f2f7633d439d6ad927be

for ITK : (git version)
404ec83fa42fcef4d69ee3be526e9c75ae958fb5

for GoFigure2 : (git version)
93557927134b4f7f8847c3418af851931369bad6

Antonin

[antonin perrot-audet]

Funny thing, I just tried to compile everything with options provided in
the developper setup :
ITK version (v3.20.0)
VTK version (v5.6.1)
Gofigure (latest on master)

I used these options :
VTK :
VTK_USE_GUISUPPORT ON # NOT REQUIRED WITH GIT ANYMORE (01-27-2011)
VTK_USE_QT ON
VTK_USE_MYSQL ON
VTK_USE_PARALLEL ON # NOT REQUIRED WITH GIT ANYMORE (01-27-2011)
VTK_USE_FFMPEG_ENCODER ON # NOT REQUIRED WITH GIT ANYMORE (01-27-2011)

ITK :
ITK_USE_REVIEW ON
ITK_USE_REVIEW_STATISTICS ON # only for older version of ITK

and got :
Linking CXX executable ../bin/gofigure
/usr/bin/ld: cannot find -lQVTK
collect2: ld returned 1 exit status
make[2]: *** [bin/gofigure] Error 1
make[1]: *** [Main/CMakeFiles/gofigure.dir/all] Error 2
make: *** [all] Error 2

[antonin perrot-audet]

and executing this command (to verify I got the good libraries) :

gave me :

Reading package lists... Done
Building dependency tree
Reading state information... Done
build-essential is already the newest version.
ffmpeg is already the newest version.
libavcodec-dev is already the newest version.
libavformat-dev is already the newest version.
libavutil-dev is already the newest version.
libboost-dev is already the newest version.
libswscale-dev is already the newest version.
libxt-dev is already the newest version.
libxt-dev set to manually installed.
cmake is already the newest version.
git is already the newest version.
libmysqlclient-dev is already the newest version.
libqt4-dev is already the newest version.
mysql-common is already the newest version.
mysql-common set to manually installed.
mysql-server is already the newest version.
qt4-doc is already the newest version.
qt4-doc set to manually installed.
uuid-dev is already the newest version.
cmake-curses-gui is already the newest version.
The following extra packages will be installed:
libossp-uuid16
The following NEW packages will be installed:
libossp-uuid16 uuid
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 83.4kB of archives.
After this operation, 254kB of additional disk space will be used.

So no big deal, just an update, it seems like I've got what it takes to
compile GoFigure2 ?

[Arnaud GELAS]

Antonin,

Can you tell me which OS you are using, please?
Is it Ubuntu 10.10, 64 bits?

I'll set up a virtualbox!

Thanks,
Arnaud

[antonin perrot-audet]

Ok, first good news : it seems like installing

The following extra packages will be installed:
libossp-uuid16
The following NEW packages will be installed:
libossp-uuid16 uuid

fixed it !

I could compile and run GoFigure2 and even open an image !
I'll now try with newer tags of VTK and ITK and let you know.

[Arnaud GELAS]

Excellent :) !

Please let us know how it goes

[antonin perrot-audet]

Cool, I used the latest tag of ITK and VTK from git, and compiled
Gofigure2 with success in RELEASE !
I can open an image, I don't have any segmentation or tool option
available ? is it in plugins now ?
Still a tiny detail : opening and closing (with the cross or cancel) the
LUT widget changes the current LUT in a random manner, as well as the
ranges for intensity mappings.

Pretty happy that it works. We may think about integrating the big
images segmentation pipeline I am working on.

Cheers,

Antonin

[Arnaud GELAS]

Antonin,

Excellent news!

On 03/29/2011 12:15 PM, antonin perrot-audet wrote:
> Cool, I used the latest tag of ITK and VTK from git, and compiled
> Gofigure2 with success in RELEASE !
> I can open an image, I don't have any segmentation or tool option
> available ? is it in plugins now ?

As you know, segmentation tools are only available when you use the
Database.
Resulting traces (contours, meshes, tracks, lineages) can be re-edited
when saved in the database...

> Still a tiny detail : opening and closing (with the cross or cancel) the
> LUT widget changes the current LUT in a random manner, as well as the
> ranges for intensity mappings.

Thanks for reporting, I'll look at it now!

> Pretty happy that it works. We may think about integrating the big
> images segmentation pipeline I am working on.

It will be indeed really interesting to get your pipeline into GoFigure2!

> Cheers,
>
> Antonin

Best,
Arnaud