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IDProjectCategoryView StatusDate SubmittedLast Update
0003176Slicer4Core: MRMLpublic2013-06-18 09:292017-06-07 23:27
ReporterMarine Assigned Tojcfr  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.2.0 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0003176: Slicer crashes when saving data after manual segmentation using EditorModule
Description

It is not possible to save the data after manual segmentation.

Slicer 4.2.0-2013-06-13 r22100. Mac OSX 10.8.3

To reproduce:

  • Load CTchest data from SampleData
  • Go to EditorModule and segment the data
  • Save the Scene/LabelMap
    And it crashes...
Additional Information

Process: Slicer [1939]
Path: /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer
Identifier: ???
Version: 4.2.0 (4.2.0-2013-06-13)
Code Type: X86-64 (Native)
Parent Process: Slicer [1938]
User ID: 501

Date/Time: 2013-06-18 12:18:49.710 -0400
OS Version: Mac OS X 10.8.3 (12D78)
Report Version: 10

Interval Since Last Report: 627925 sec
Crashes Since Last Report: 103
Per-App Interval Since Last Report: 16262 sec
Per-App Crashes Since Last Report: 7
Anonymous UUID: 77B933DA-DC9A-80D2-D901-4A07274EBBBB

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000

VM Regions Near 0:
-->
__TEXT 000000010204c000-000000010207d000 [ 196K] r-x/rwx SM=COW /Users/USER/*/Slicer.app/Contents/MacOS/Slicer

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libMRMLCore.dylib 0x00000001078e30c8 vtkMRMLSelectionNode::GetUnitNodes(std::vector<vtkMRMLUnitNode, std::allocator<vtkMRMLUnitNode> >&) + 104
1 libMRMLCore.dylib 0x00000001078e2fc0 vtkMRMLSelectionNode::Copy(vtkMRMLNode) + 288
2 libMRMLCore.dylib 0x00000001078dcc02 vtkMRMLSceneViewNode::StoreScene() + 322
3 libqSlicerDataModule.dylib 0x000000011a939583 qSlicerSceneWriter::writeToMRML(QMap<QString, QVariant> const&) + 1283
4 libqSlicerDataModule.dylib 0x000000011a938e33 qSlicerSceneWriter::write(QMap<QString, QVariant> const&) + 595
5 libqSlicerBaseQTCore.dylib 0x0000000102b9c0c1 qSlicerCoreIOManager::saveNodes(QString, QMap<QString, QVariant> const&) + 289
6 libqSlicerBaseQTGUI.dylib 0x00000001023820b2 qSlicerSaveDataDialogPrivate::saveScene() + 498
7 libqSlicerBaseQTGUI.dylib 0x0000000102380862 qSlicerSaveDataDialogPrivate::accept() + 50
8 libqSlicerBaseQTGUI.dylib 0x00000001023b21a1 qSlicerSaveDataDialogPrivate::qt_static_metacall(QObject, QMetaObject::Call, int, void) + 129
9 QtCore 0x0000000109c191ee QMetaObject::activate(QObject, QMetaObject const, int, void) + 1566
10 QtCore 0x0000000109c191ee QMetaObject::activate(QObject, QMetaObject const, int, void) + 1566
11 QtGui 0x0000000109490321 QAbstractButton::clicked(bool) + 49
12 QtGui 0x00000001091b35c0 QAbstractButtonPrivate::emitClicked() + 64
13 QtGui 0x00000001091b47fa QAbstractButtonPrivate::click() + 154
14 QtGui 0x00000001091b4a51 QAbstractButton::mouseReleaseEvent(QMouseEvent) + 113
15 QtGui 0x0000000108e6c355 QWidget::event(QEvent) + 2421
16 QtGui 0x00000001091b3848 QAbstractButton::event(QEvent) + 40
17 QtGui 0x000000010924f595 QPushButton::event(QEvent) + 69
18 QtGui 0x0000000108e0f9ed QApplicationPrivate::notify_helper(QObject, QEvent) + 189
19 QtGui 0x0000000108e16590 QApplication::notify(QObject, QEvent) + 2384
20 QtCore 0x0000000109c0120c QCoreApplication::notifyInternal(QObject, QEvent) + 124
21 QtGui 0x0000000108e13fdd QApplicationPrivate::sendMouseEvent(QWidget, QMouseEvent, QWidget, QWidget, QWidget, QPointer<QWidget>&, bool) + 333
22 QtGui 0x0000000108dc3acb qt_mac_handleMouseEvent(NSEvent, QEvent::Type, Qt::MouseButton, QWidget, bool) + 763
23 com.apple.AppKit 0x00007fff8f2fc606 -[NSWindow sendEvent:] + 7053
24 QtGui 0x0000000108db06b7 -[QCocoaPanel sendEvent:] + 87
25 com.apple.AppKit 0x00007fff8f2f8674 -[NSApplication sendEvent:] + 5761
26 QtGui 0x0000000108dbdbf4 -[QNSApplication sendEvent:] + 84
27 com.apple.AppKit 0x00007fff8f46169a -[NSApplication _realDoModalLoop:peek:] + 582
28 com.apple.AppKit 0x00007fff8f461d6e -[NSApplication runModalSession:] + 49
29 QtGui 0x0000000108dc88ee QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1422
30 QtCore 0x0000000109c00114 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68
31 QtCore 0x0000000109c004c4 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
32 QtGui 0x00000001092b7d55 QDialog::exec() + 229
33 libqSlicerBaseQTGUI.dylib 0x00000001023842fb qSlicerSaveDataDialog::exec(QMap<QString, QVariant> const&) + 43
34 libqSlicerBaseQTGUI.dylib 0x0000000102361a23 qSlicerIOManager::openDialog(QString, qSlicerFileDialog::IOAction, QMap<QString, QVariant>) + 499
35 libqSlicerApp.dylib 0x00000001020c7b1f qSlicerIOManager::openSaveDataDialog() + 79
36 QtCore 0x0000000109c191ee QMetaObject::activate(QObject, QMetaObject const, int, void*) + 1566
37 QtGui 0x0000000108e09431 QAction::triggered(bool) + 49
38 QtGui 0x0000000108e0a7c4 QAction::activate(QAction::ActionEvent) + 180
39 QtGui 0x00000001091b47b9 QAbstractButtonPrivate::click() + 89
40 QtGui 0x00000001091b4a51 QAbstractButton::mouseReleaseEvent(QMouseEvent) + 113
41 QtGui 0x0000000109282cd2 QToolButton::mouseReleaseEvent(QMouseEvent) + 18
42 QtGui 0x0000000108e6c355 QWidget::event(QEvent) + 2421
43 QtGui 0x00000001091b3848 QAbstractButton::event(QEvent) + 40
44 QtGui 0x00000001092850df QToolButton::event(QEvent) + 63
45 QtGui 0x0000000108e0f9ed QApplicationPrivate::notify_helper(QObject, QEvent) + 189
46 QtGui 0x0000000108e16590 QApplication::notify(QObject, QEvent) + 2384
47 QtCore 0x0000000109c0120c QCoreApplication::notifyInternal(QObject, QEvent) + 124
48 QtGui 0x0000000108e13fdd QApplicationPrivate::sendMouseEvent(QWidget, QMouseEvent, QWidget, QWidget, QWidget*, QPointer<QWidget>&, bool) + 333
49 QtGui 0x0000000108dc3acb qt_mac_handleMouseEvent(NSEvent, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 763
50 com.apple.AppKit 0x00007fff8f2fc606 -[NSWindow sendEvent:] + 7053
51 QtGui 0x0000000108db8bb7 -[QCocoaWindow sendEvent:] + 87
52 com.apple.AppKit 0x00007fff8f2f8674 -[NSApplication sendEvent:] + 5761
53 QtGui 0x0000000108dbdbf4 -[QNSApplication sendEvent:] + 84
54 com.apple.AppKit 0x00007fff8f20e24a -[NSApplication run] + 636
55 QtGui 0x0000000108dc8a80 QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1824
56 QtCore 0x0000000109c00114 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68
57 QtCore 0x0000000109c004c4 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
58 QtCore 0x0000000109c02bac QCoreApplication::exec() + 188
59 0x000000010207b1df main + 4159
60 0x000000010207a194 start + 52

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff86a35d16 kevent + 10
1 libdispatch.dylib 0x00007fff8c478dea _dispatch_mgr_invoke + 883
2 libdispatch.dylib 0x00007fff8c4789ee _dispatch_mgr_thread + 54

Thread 2:: ctkFDHandler
0 libsystem_kernel.dylib 0x00007fff86a35ffa read + 10
1 libCTKCore.0.1.dylib 0x0000000106809ad0 ctkFDHandler::run() + 80
2 QtCore 0x0000000109ae6f74 QThreadPrivate::start(void*) + 356
3 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
4 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 3:: ctkFDHandler
0 libsystem_kernel.dylib 0x00007fff86a35ffa read + 10
1 libCTKCore.0.1.dylib 0x0000000106809ad0 ctkFDHandler::run() + 80
2 QtCore 0x0000000109ae6f74 QThreadPrivate::start(void*) + 356
3 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
4 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fff86a35386 __semwait_signal + 10
1 libsystem_c.dylib 0x00007fff8c0ec800 nanosleep + 163
2 libsystem_c.dylib 0x00007fff8c0ec717 usleep + 54
3 libSlicerBaseLogic.dylib 0x0000000105067fd7 vtkSlicerApplicationLogic::ProcessProcessingTasks() + 359
4 libSlicerBaseLogic.dylib 0x0000000105067ccc vtkSlicerApplicationLogic::ProcessingThreaderCallback(void*) + 28
5 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
6 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 5:
0 libsystem_kernel.dylib 0x00007fff86a35386 __semwait_signal + 10
1 libsystem_c.dylib 0x00007fff8c0ec800 nanosleep + 163
2 libsystem_c.dylib 0x00007fff8c0ec717 usleep + 54
3 libSlicerBaseLogic.dylib 0x0000000105068177 vtkSlicerApplicationLogic::ProcessNetworkingTasks() + 359
4 libSlicerBaseLogic.dylib 0x0000000105067cfc vtkSlicerApplicationLogic::NetworkingThreaderCallback(void*) + 28
5 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
6 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 6:
0 libsystem_kernel.dylib 0x00007fff86a350fa __psynch_cvwait + 10
1 libsystem_c.dylib 0x00007fff8c066fe9 _pthread_cond_wait + 869
2 QtWebKit 0x0000000103d13845 WTF::TCMalloc_PageHeap::scavengerThread() + 117
3 QtWebKit 0x0000000103d13ad9 WTF::TCMalloc_PageHeap::runScavengerThread(void*) + 9
4 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
5 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 7:: QThread
0 libsystem_kernel.dylib 0x00007fff86a35322 __select + 10
1 QtCore 0x0000000109c3248e qt_safe_select(int, fd_set, fd_set, fd_set, timeval const) + 142
2 QtCore 0x0000000109c35f45 QEventDispatcherUNIXPrivate::doSelect(QFlags<QEventLoop::ProcessEventsFlag>, timeval) + 389
3 QtCore 0x0000000109c368b2 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 178
4 QtCore 0x0000000109c00114 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68
5 QtCore 0x0000000109c004c4 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
6 QtCore 0x0000000109ae4358 QThread::exec() + 312
7 QtCore 0x0000000109ae6f74 QThreadPrivate::start(void) + 356
8 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
9 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 8:: QProcessManager
0 libsystem_kernel.dylib 0x00007fff86a35322 __select + 10
1 QtCore 0x0000000109bd44d0 QProcessManager::run() + 96
2 QtCore 0x0000000109ae6f74 QThreadPrivate::start(void*) + 356
3 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
4 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 9:: com.apple.CFSocket.private
0 libsystem_kernel.dylib 0x00007fff86a35322 select + 10
1 com.apple.CoreFoundation 0x00007fff885c6f46 CFSocketManager + 1302
2 libsystem_c.dylib 0x00007fff8c0627a2 _pthread_start + 327
3 libsystem_c.dylib 0x00007fff8c04f1e1 thread_start + 13

Thread 10:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 11:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 12:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 13:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 14:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 15:
0 libsystem_kernel.dylib 0x00007fff86a356d6 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8c064f4c _pthread_workq_return + 25
2 libsystem_c.dylib 0x00007fff8c064d13 _pthread_wqthread + 412
3 libsystem_c.dylib 0x00007fff8c04f1d1 start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007f9695fde770 rcx: 0x000000000000002f rdx: 0x0000000000000000
rdi: 0x00007f9695fde75d rsi: 0x00007f96999d3d7d rbp: 0x00007fff5dbafd00 rsp: 0x00007fff5dbafcb0
r8: 0x0000000000000001 r9: 0x0000000000000018 r10: 0x00007fff9362563f r11: 0x00007fff8e068010
r12: 0x00007f9695b73840 r13: 0x0000000000000000 r14: 0x00007f9695b73878 r15: 0x00007fff5dbafd20
rip: 0x00000001078e30c8 rfl: 0x0000000000010246 cr2: 0x0000000000000000
Logical CPU: 2

Binary Images:
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0x117451000 - 0x117486ff7 +vtkSlicerDataModuleLogicPython.so (???) <5671F2EF-7D34-3801-8493-72E460FC65D9> /Users/USER//vtkSlicerDataModuleLogicPython.so
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0x1174f5000 - 0x11752aff7 +vtkSlicerDoubleArraysModuleLogicPython.so (???) <9CDEB6A8-5E78-30EB-8C0C-E583E9E4166A> /Users/USER//vtkSlicerDoubleArraysModuleLogicPython.so
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0x11829e000 - 0x1182d4ff7 +vtkSlicerOpenIGTLinkIFModuleLogicPython.so (???) <2580C196-799A-3F9A-A87B-9989E7895965> /Users/USER//vtkSlicerOpenIGTLinkIFModuleLogicPython.so
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0x118315000 - 0x118348ff7 +libvtkSlicerOpenIGTLinkIFModuleLogic.dylib (0) <4FABF988-87EB-3C5F-86FB-DD2E9F4E9937> /Users/USER//libvtkSlicerOpenIGTLinkIFModuleLogic.dylib
0x118350000 - 0x11838cfff +libvtkSlicerOpenIGTLinkIFModuleMRMLPythonD.dylib (0) <0FBABD84-77CA-3820-8CB3-0E4066AABE71> /Users/USER//libvtkSlicerOpenIGTLinkIFModuleMRMLPythonD.dylib
0x118398000 - 0x1183d8ff7 +libvtkSlicerOpenIGTLinkIFModuleMRML.dylib (0) <45D71F71-DE18-327E-9572-63CFC533A7E9> /Users/USER//libvtkSlicerOpenIGTLinkIFModuleMRML.dylib
0x1183f4000 - 0x118435ff7 +libOpenIGTLink.1.dylib (1.9.8) <3E4C9501-1E18-3BD1-A982-31FB6DF195CB> /Users/USER//libOpenIGTLink.1.dylib
0x11845a000 - 0x11848ffff +vtkSlicerReformatModuleLogicPython.so (???) <8ACA38D9-4

TagsSummer AHM 2013

Relationships

related to 0003152 closedfinetjul Slicer crashes with "Close Scene" and "Application Settings Cancel" 

Activities

jcfr

jcfr

2013-06-19 11:59

administrator   ~0008789

Fixed in 22108
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=22108
jcfr

jcfr

2014-03-06 04:56

administrator   ~0010796

Closing resolved issues that have not been updated in more than 3 months
jcfr

jcfr

2017-06-07 23:27

administrator   ~0014641

Fix committed to 2145-support-for-installing-extension-from-file branch.

Related Changesets

Slicer: 2145-support-for-installing-extension-from-file 12fdccd4

2013-06-19 15:58:21

jcfr

Details Diff 		BUG: Fix crash when saving data

Commit r22095[1] intended to disable "unit" functionality by
preventing the associated logic from being loaded.

This commit comments the "unit" code associated with the selection node
to fix crash happening when saving data.

See http://www.na-mic.org/Bug/view.php?id=3176
Fixes 0003176

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22095

Co-authored-by: Marine Clogenson <marine.clogenson@epfl.ch>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22108 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSelectionNode.cxx Diff File

Issue History

Date Modified Username Field Change
2013-06-18 09:29 Marine New Issue
2013-06-18 09:29 Marine Status new => assigned
2013-06-18 09:29 Marine Assigned To => alexy
2013-06-19 07:35 jcfr Assigned To alexy => jcfr
2013-06-19 07:35 jcfr Target Version => Slicer 4.3.0
2013-06-19 10:23 jcfr Relationship added related to 0003152
2013-06-19 11:59 jcfr Note Added: 0008789
2013-06-19 11:59 jcfr Status assigned => resolved
2013-06-19 11:59 jcfr Fixed in Version => Slicer 4.3.0
2013-06-19 11:59 jcfr Resolution open => fixed
2013-06-19 21:55 jcfr Tag Attached: Summer AHM 2013
2014-03-06 04:56 jcfr Note Added: 0010796
2014-03-06 04:58 jcfr Status resolved => closed
2017-06-07 23:27 jcfr Changeset attached => Slicer 2145-support-for-installing-extension-from-file 12fdccd4
2017-06-07 23:27 jcfr Note Added: 0014641