[Insight-users] problem with Morphogenesis
Pavel Tomancak
tomancak at mpi-cbg.de
Tue Jan 24 12:13:23 EST 2006
My experience with C++ is very limited, so some of this may sound a bit
naive. I am a biologist after all.
I downloaded InsightToolkit-2.4.0 and compiled it into
/Applications/itk_binary on Mac OS X 10.3.9 with Xcode 1.5 and upgraded
gcc to 3.3. I used the default cmake options, no Examples, no Tests.
Everything seems fine after make, which I suspect means nothing. Hello
World works.
Now, I downloaded the InsightApplications-2.4.0, meddled slightly with
CMakeLists.txt to skip to the Morphogenesis part. (I comment every
SUBDIR before Morphogenesis, otherwise it takes too long to get there,
couldn't figure any other way).
I installed fltk-1.1.7 and pointed cmake to it, I also change the
USE_FLTK to ON.
Now I run make in the dir where I unpackaged the InsightApplication,
again everything seems fine, voila - a Morphogenesis application
appears.
It starts, windows appear, images can be loaded, zoomed and so on. I
can create any species egg I want, but, now it comes, after clicking on
play it invariantly crashes.
Below please find the error messages which are truly incomprehensible
to me. They are not always the same, but often there is a line like
this
0 libITKCommon.dylib 0x013a1228
itk::RealTimeClock::GetTimeStamp() const + 0x78
I would appreciate any help, this whole application of cellular
automata to image processing is totally fascinating. I am very eager to
try it on my images.
Thanks in advance
PAvel
Here comes the error message
Date/Time: 2006-01-24 17:57:06 +0100
OS Version: 10.3.9 (Build 7W98)
Report Version: 2
Command: Morphogenesis
Path:
/Users/tomancak/Desktop/InsightApplications-2.4.0/Morphogenesis/
Morphogenesis
Version: ??? (???)
PID: 10843
Thread: 0
Exception: EXC_BAD_ACCESS (0x0001)
Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x00000048
Thread 0 Crashed:
0 libITKCommon.dylib 0x013a1228
itk::RealTimeClock::GetTimeStamp() const + 0x78
1 Morphogenesis 0x00007eb8
bio::CellsViewerBase::GetElapsedTime() const + 0x34
2 Morphogenesis 0x00009708
bio::CellsViewerCommand::Execute(itk::Object const*, itk::EventObject
const&) + 0xd4
3 Morphogenesis 0x00009828
bio::CellsViewerCommand::Execute(itk::Object*, itk::EventObject const&)
+ 0x50
4 libITKCommon.dylib 0x01396f74
itk::SubjectImplementation::InvokeEvent(itk::EventObject const&,
itk::Object*) + 0xe8
5 libITKCommon.dylib 0x0139802c
itk::Object::InvokeEvent(itk::EventObject const&) + 0x40
6 Morphogenesis 0x0000b47c
bio::CellularAggregate::AdvanceTimeStep() + 0x1cc
7 Morphogenesis 0x0000782c
bio::CellsViewerBase::Run() + 0xbc
8 Morphogenesis 0x00009204 bio::CellsViewer::Run()
+ 0x20
9 Morphogenesis 0x00010a00
CellsViewerGUI::cb_3_i(Fl_Button*, void*) + 0x40
10 Morphogenesis 0x00010a58
CellsViewerGUI::cb_3(Fl_Button*, void*) + 0x44
11 Morphogenesis 0x0004061c Fl_Button::handle(int) +
0x3cc
12 Morphogenesis 0x00021998 send(int, Fl_Widget*,
Fl_Window*) + 0xc0
13 Morphogenesis 0x00021cf4 Fl::handle(int,
Fl_Window*) + 0x33c
14 Morphogenesis 0x00024268
carbonMouseHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*)
+ 0x2dc
15 <<00000000>> 0x92882e50 0 + 0x92882e50
16 <<00000000>> 0x928830c4 0 + 0x928830c4
17 <<00000000>> 0x92895530 0 + 0x92895530
18 Morphogenesis 0x0002342c
carbonDispatchHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*,
void*) + 0xf0
19 <<00000000>> 0x92882e50 0 + 0x92882e50
20 <<00000000>> 0x928830c4 0 + 0x928830c4
21 <<00000000>> 0x92895530 0 + 0x92895530
22 Morphogenesis 0x000238a4 do_queued_events(double)
+ 0x178
23 Morphogenesis 0x00023998 fl_wait(double) + 0x1c
24 Morphogenesis 0x00020f1c Fl::wait(double) + 0x84
25 Morphogenesis 0x00020f8c Fl::run() + 0x38
26 Morphogenesis 0x0000facc main + 0x34c
27 Morphogenesis 0x00003204 _start + 0x188
(crt.c:267)
28 dyld 0x8fe1a278 _dyld_start + 0x64
Thread 1:
0 libSystem.B.dylib 0x900078b8 mach_msg_trap + 0x8
1 libSystem.B.dylib 0x90007438 mach_msg + 0x38
2 com.unsanity.ape 0xc0002c14 __ape_internal + 0xce4
3 com.unsanity.ape 0xc0001a28 __ape_agent + 0x40
4 libSystem.B.dylib 0x90024990 _pthread_body + 0x28
Thread 2:
0 libSystem.B.dylib 0x900078b8 mach_msg_trap + 0x8
1 libSystem.B.dylib 0x90007438 mach_msg + 0x38
2 ...lagutin.audio_hijack.server 0x01194e60 ah_serv_loop + 0x58
3 libSystem.B.dylib 0x90024990 _pthread_body + 0x28
PPC Thread State:
srr0: 0x013a1228 srr1: 0x0200f030 vrsave: 0x00000000
cr: 0x82822222 xer: 0x20000004 lr: 0x013a11dc ctr: 0x90008b60
r0: 0x800eeea0 r1: 0xbffff040 r2: 0x00000000 r3: 0x00000000
r4: 0x00000000 r5: 0x00000000 r6: 0x0006b2df r7: 0x43d65c61
r8: 0x000eeea0 r9: 0x015311c8 r10: 0x43300000 r11: 0x007b77ee
r12: 0x000f4240 r13: 0x00000000 r14: 0x00000000 r15: 0x00000000
r16: 0x00000000 r17: 0x00000000 r18: 0x00000000 r19: 0x00000000
r20: 0x00000002 r21: 0x00000000 r22: 0x0396b290 r23: 0x03929a00
r24: 0xbffff7c0 r25: 0x00000030 r26: 0x0000002f r27: 0x00128a3c
r28: 0x00128a40 r29: 0xbffff310 r30: 0xbffff040 r31: 0x013a11c8
Binary Images Description:
0x1000 - 0x126fff Morphogenesis
/Users/tomancak/Desktop/InsightApplications-2.4.0/Morphogenesis/
Morphogenesis
0x24c000 - 0x24dfff libITKznz.dylib
/Applications/itk_binary/bin/libITKznz.dylib
0x267000 - 0x282fff libITKniftiio.dylib
/Applications/itk_binary/bin/libITKniftiio.dylib
0x298000 - 0x2c8fff libITKNrrdIO.dylib
/Applications/itk_binary/bin/libITKNrrdIO.dylib
0x2e8000 - 0x2fafff libitkzlib.dylib
/Applications/itk_binary/bin/libitkzlib.dylib
0x405000 - 0x43bfff libitkjpeg12.dylib
/Applications/itk_binary/bin/libitkjpeg12.dylib
0x444000 - 0x47afff libitkjpeg16.dylib
/Applications/itk_binary/bin/libitkjpeg16.dylib
0x483000 - 0x4affff libitkpng.dylib
/Applications/itk_binary/bin/libitkpng.dylib
0x4b7000 - 0x4e6fff libITKEXPAT.dylib
/Applications/itk_binary/bin/libITKEXPAT.dylib
0x4ee000 - 0x559fff libITKAlgorithms.dylib
/Applications/itk_binary/bin/libITKAlgorithms.dylib
0x5d7000 - 0x633fff libITKBasicFilters.dylib
/Applications/itk_binary/bin/libITKBasicFilters.dylib
0x69e000 - 0x6fbfff libITKStatistics.dylib
/Applications/itk_binary/bin/libITKStatistics.dylib
0x766000 - 0x79cfff libitkjpeg8.dylib
/Applications/itk_binary/bin/libitkjpeg8.dylib
0x1008000 - 0x1068fff libitktiff.dylib
/Applications/itk_binary/bin/libitktiff.dylib
0x1190000 - 0x1197fff alex_lagutin.audio_hijack.server
1.2.9 /Library/Application Enhancers/Instant Hijack
Server.ape/Contents/MacOS/Instant Hijack Server
0x11cd000 - 0x126efff libITKSpatialObject.dylib
/Applications/itk_binary/bin/libITKSpatialObject.dylib
0x134c000 - 0x1365fff GLDriver
/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/
GLDriver.bundle/GLDriver
0x1384000 - 0x1536fff libITKCommon.dylib
/Applications/itk_binary/bin/libITKCommon.dylib
0x1700000 - 0x189afff libITKIO.dylib
/Applications/itk_binary/bin/libITKIO.dylib
0x1a49000 - 0x1b4cfff libitkgdcm.dylib
/Applications/itk_binary/bin/libitkgdcm.dylib
0x1c44000 - 0x1c96fff libitkvcl.dylib
/Applications/itk_binary/bin/libitkvcl.dylib
0x1d73000 - 0x1d8dfff GLRendererFloat
/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/
GLRendererFloat.bundle/GLRendererFloat
0x1dc8000 - 0x1e89fff libITKNumerics.dylib
/Applications/itk_binary/bin/libITKNumerics.dylib
0x1f4d000 - 0x2005fff libitkvnl_inst.dylib
/Applications/itk_binary/bin/libitkvnl_inst.dylib
0x20ba000 - 0x2174fff libitkvnl_algo.dylib
/Applications/itk_binary/bin/libitkvnl_algo.dylib
0x2229000 - 0x2298fff libitksys.dylib
/Applications/itk_binary/bin/libitksys.dylib
0x23b5000 - 0x2520fff libitknetlib.dylib
/Applications/itk_binary/bin/libitknetlib.dylib
0x2563000 - 0x25fdfff libITKDICOMParser.dylib
/Applications/itk_binary/bin/libITKDICOMParser.dylib
0x26de000 - 0x27a5fff libITKMetaIO.dylib
/Applications/itk_binary/bin/libITKMetaIO.dylib
0x28d4000 - 0x2c56fff libitkvnl.dylib
/Applications/itk_binary/bin/libitkvnl.dylib
0x5dac000 - 0x5ea1fff GLEngine
/System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/
GLEngine
0x5f8a000 - 0x6060fff ATIRadeon9700GLDriver
/System/Library/Extensions/ATIRadeon9700GLDriver.bundle/Contents/
MacOS/ATIRadeon9700GLDriver
0x61fd000 - 0x628cfff GLRasterARGB8888D32
/System/Library/Frameworks/OpenGL.framework/Resources/
GLRasterARGB8888D32.bundle/GLRasterARGB8888D32
0x80830000 - 0x8090efff libxml2.2.dylib /usr/lib/libxml2.2.dylib
0x8134c000 - 0x8134dfff libGLSystem.dylib
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
libGLSystem.dylib
0x83b6c000 - 0x83b78fff com.apple.agl 2.5
(AGL-2.5) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x84cab000 - 0x84d9cfff libGLProgrammability.dylib
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
libGLProgrammability.dylib
0x8fe00000 - 0x8fe4ffff dyld /usr/lib/dyld
0x90000000 - 0x9014ffff libSystem.B.dylib /usr/lib/libSystem.B.dylib
0x901c0000 - 0x9026dfff com.apple.CoreFoundation 6.3.8
(299.36) /System/Library/Frameworks/CoreFoundation.framework/Versions/
A/CoreFoundation
0x902b0000 - 0x90529fff com.apple.CoreServices.CarbonCore
10.3.7 /System/Library/Frameworks/CoreServices.framework/Versions/A/
Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x90584000 - 0x905f3fff com.apple.framework.IOKit 1.3.6
(???) /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x90610000 - 0x9069afff com.apple.CoreServices.OSServices
3.0.1 /System/Library/Frameworks/CoreServices.framework/Versions/A/
Frameworks/OSServices.framework/Versions/A/OSServices
0x90700000 - 0x90700fff com.apple.CoreServices 10.3
(???) /System/Library/Frameworks/CoreServices.framework/Versions/A/
CoreServices
0x90702000 - 0x90769fff com.apple.audio.CoreAudio
2.1.3 /System/Library/Frameworks/CoreAudio.framework/Versions/A/
CoreAudio
0xc0000000 - 0xc000ffff com.unsanity.ape
1.4.6 /Library/Frameworks/ApplicationEnhancer.framework/Versions/A/
ApplicationEnhancer
------------------------------------------------------------------------
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Pavel Tomancak, Ph.D.
Group Leader
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden Tel.: +49 351 210 2670
Germany Fax: +49 351 210 2020
tomancak at mpi-cbg.de
http://www.mpi-cbg.de
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