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[Seg3D] Re: build problems on 9.10 Ubuntu ?

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  • From: Kristen Zygmunt <>
  • To:
  • Subject: [Seg3D] Re: build problems on 9.10 Ubuntu ?
  • Date: Thu, 25 Feb 2010 16:23:30 -0700

Hi Alex,
Seg3D delegates file reading and writing to ITK's ImageIO factory structure for nearly all file formats including .lsm. According to the discussion thread at , the ITK TIFF/LSM reader does not handle multi-channel data. Therefore, if your data is multichannel, then this most likely explains the Seg3D crash. The discussion thread also mentions that Wisconsin has a preliminary version of an ITK ImageIO class that could handle these files, but is not clear to me what the plan is for integration of the Wisconsin Image IO code into the ITK distribution, thus making it available to Seg3D.

Have you tried using Seg3D to open the TIFF file that is produced from bfconvert? If that works, then a temporary solution may be to run bfconvert first prior to using Seg3D. However, you may still run into the same multi-channel issue. In that case, each channel may need to be saved into a separate file.


On Feb 25, 2010, at 3:05 PM, <> < > wrote:


I have built seg3D on a 9.10 Ubuntu machine (had to manually set symbolic links
to libtiff and libjpeg so ITK could find them) but it is crashing after trying
uploading a .lsm file. Any ideas on what could be the problem ? The .lsm seems
to be OK as we could visualize and convert it using bfconvert from the
Wisconsin group.

- Alex.

cell [271] : ./Seg3D &                                                      
[1] 25887                                                               
cell [272] :                                                            
Thread "main" (id: 140330413525024, pid: 25887)                       
        caught signal SIGSEGV at address 0x7fa12529b010 (segmentation
1. ./Seg3D                                                              
 in SCIRun::handle_abort_signals(int, siginfo*, void*)          
2. /lib/ [0x7fa1339eb040]                                      
3. ./Seg3D                                                              
 in itk::TIFFImageIO::ReadVolume(void*)                         
4. ./Seg3D                                                              
 in itk::TIFFImageIO::Read(void*)                                       
5. ./Seg3D                                                              
 in itk::ImageFileReader<itk::Image<float, 3u>,
itk::DefaultConvertPixelTraits<float> >::GenerateData()                
6. ./Seg3D                                                              
 in itk::ProcessObject::UpdateOutputData(itk::DataObject*)              
7. ./Seg3D                                                              
 in SCIRun::LockingHandle<SCIRun::NrrdVolume>
SCIRun::Painter::load_volume<float>(std::string, int&)                        
8. ./Seg3D                                                              
 in SCIRun::Painter::LoadVolume(std::string const&)                 
9. ./Seg3D                                                              
in SCIRun::Painter::LoadVolume(SCIRun::LockingHandle<SCIRun::BaseEvent>&)
a. ./Seg3D                                                              
SCIRun::Skinner::CallbackT<SCIRun::Painter>::operator() (SCIRun::LockingHandle<SCIRun::BaseEvent>&)
b. ./Seg3D                                                              
SCIRun ::Skinner ::SignalThrower::throw_signal(std::list<SCIRun::Skinner::Callback*,
std::allocator<SCIRun::Skinner::Callback*> >&,
c. ./Seg3D                                                              
 in SCIRun::Skinner::SignalThrower::throw_signal(std::map<std::string,
std::allocator<SCIRun::Skinner::Callback*> >, std::less<std::string>,
std::allocator<std::pair<std::string const,
std::allocator<SCIRun::Skinner::Callback*> > > > >&,
d. ./Seg3D                                                              
 in SCIRun::Skinner::Drawable::throw_signal(std::string const&)     
e. ./Seg3D                                                              
in SCIRun::Painter::ThrowSkinnerSignal(SCIRun::ThrowSkinnerSignalEvent*,
f. ./Seg3D
 in SCIRun::Seg3DFrame::FileLoadVolume(wxCommandEvent&)
10. ./Seg3D
 in wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const&,
wxEvtHandler*, wxEvent&)
11. ./Seg3D
 in wxEventHashTable::HandleEvent(wxEvent&, wxEvtHandler*)
12. ./Seg3D
 in wxEvtHandler::ProcessEvent(wxEvent&)
13. ./Seg3D [0xcd9145]
14. /usr/lib/ [0x7fa13678e27d]
15. /usr/lib/ [0x7fa1367a3e3b]
16. /usr/lib/ [0x7fa1367a5432]
17. /usr/lib/ [0x7fa1367a5953]
18. /usr/lib/ [0x7fa137eb59eb]
19. /usr/lib/
1a. /usr/lib/ [0x7fa137db7875]
1b. /usr/lib/ [0x7fa137da7df8]
1c. /usr/lib/ [0x7fa13678e27d]
1d. /usr/lib/ [0x7fa1367a3b1e]
1e. /usr/lib/ [0x7fa1367a52bd]
1f. /usr/lib/ [0x7fa1367a5953]
20. /usr/lib/ [0x7fa137eb009e]
21. /usr/lib/ [0x7fa137da0693]
22. /usr/lib/ [0x7fa137da17b3]
23. /usr/lib/ [0x7fa137a1af3c]
24. /usr/lib/ [0x7fa135ee520a]
25. /usr/lib/ [0x7fa135ee88e0]
26. /usr/lib/ [0x7fa135ee8dad]
27. /usr/lib/ [0x7fa137da1bc7]
28. ./Seg3D
 in wxEventLoop::Run()
29. ./Seg3D
 in wxAppBase::MainLoop()
2a. ./Seg3D
 in wxEntry(int&, char**)
2b. ./Seg3D(main+0x12) [0x735b32]
2c. /lib/ [0x7fa1339d65a6]
2d. ./Seg3D [0x7359b9]
140330413525024:main( RUNNING, List: )
140330231716176:Seg3D Event Processor(detached, BLOCKING, Timed wait, List: )
140330226776400:Seg3D Redraw( BLOCKING, Timed wait, List: )
140330225723728:Event Manager( BLOCKING, EventManager, List: )

Abort signalled by pid: 25887
Occured for thread: "main"

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