text:
[DB] Import of heavy VTK fails

According to Hubert, the import of (imported) heavy vtk files is crashing. It does not crash with mha or MAIN files.

I do not succeed to crash the app importing heavy vtk files. I asked hubert if he could send me these files.

ce vtk crashe MUSIC, mais il n'est pas "heavy", je ne sais pas si c'est relié.
seg_cropped.vtk.zip
Process:               MUSIC [8458]
Path:                  /Applications/MUSIC.app/Contents/MacOS/MUSIC
Identifier:            ???
Version:               ??? (???)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           MUSIC [8458]
User ID:               501
Date/Time:             2017-04-24 13:15:03.210 +0200
OS Version:            Mac OS X 10.11.6 (15G1421)
Report Version:        11
Anonymous UUID:        F5688092-F313-9033-C19A-5EBDB569A5A1
Sleep/Wake UUID:       14507A6C-109A-4CC4-9EA7-26579152DEFF
Time Awake Since Boot: 8600 seconds
Time Since Wake:       730 seconds
System Integrity Protection: enabled
Crashed Thread:        0  Dispatch queue: com.apple.main-thread
Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x00007fa6b46dcd78
Exception Note:        EXC_CORPSE_NOTIFY
VM Regions Near 0x7fa6b46dcd78:
MALLOC_SMALL           00007f9eb5800000-00007f9eb6000000 [ 8192K] rw-/rwx SM=PRV
-->
STACK GUARD            00007fff56e95000-00007fff5a695000 [ 56.0M] ---/rwx SM=NUL  stack guard for thread 0
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libvtkGraphics.5.10.dylib     	0x000000010f5c91ef vtkDataSetSurfaceFilter::UnstructuredGridExecute(vtkDataSet*, vtkPolyData*) + 10015
1   libvtkGraphics.5.10.dylib     	0x000000010f5c4849 vtkDataSetSurfaceFilter::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 1241
2   libvtkFiltering.5.10.dylib    	0x0000000110411d15 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 69
3   libvtkFiltering.5.10.dylib    	0x000000011040523d vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 61
4   libvtkFiltering.5.10.dylib    	0x000000011040492f vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 1327
5   libvtkFiltering.5.10.dylib    	0x0000000110591aa0 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 608
6   libvtkFiltering.5.10.dylib    	0x000000011041198e vtkExecutive::ForwardUpstream(vtkInformation*) + 430
7   libvtkFiltering.5.10.dylib    	0x000000011040477f vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 895
8   libvtkFiltering.5.10.dylib    	0x0000000110591aa0 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 608
9   libvtkFiltering.5.10.dylib    	0x000000011041198e vtkExecutive::ForwardUpstream(vtkInformation*) + 430
10  libvtkFiltering.5.10.dylib    	0x000000011040477f vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 895
11  libvtkFiltering.5.10.dylib    	0x0000000110591aa0 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 608
12  libvtkFiltering.5.10.dylib    	0x0000000110404f46 vtkDemandDrivenPipeline::UpdateData(int) + 246
13  libvtkFiltering.5.10.dylib    	0x0000000110591e67 vtkStreamingDemandDrivenPipeline::Update(int) + 119
14  libvtkRendering.5.10.dylib    	0x000000010f225b89 vtkPolyDataMapper::GetBounds() + 41
15  libvtkRendering.5.10.dylib    	0x000000010f15b100 vtkActor::GetBounds() + 64
16  libvtkRendering.5.10.dylib    	0x000000010f23d46c vtkRenderer::ComputeVisiblePropBounds(double*) + 156
17  libvtkRendering.5.10.dylib    	0x000000010f23cf55 vtkRenderer::ResetCamera() + 37
18  libmedVtkInria.dylib          	0x000000010e506f7f vtkImageView::ResetCamera() + 127
19  libvtkDataMeshPlugin.dylib    	0x000000011810c19d vtkDataMeshInteractor::updatePipeline() + 381
20  libvtkDataMeshPlugin.dylib    	0x000000011810bf6d vtkDataMeshInteractor::setInputData(medAbstractData*) + 237
21  libmedCore.dylib              	0x00000001081fcb7c medAbstractImageView::initialiseInteractors(medAbstractData*) + 796
22  libmedCore.dylib              	0x0000000108201e85 medAbstractLayeredView::insertLayer(unsigned int, medAbstractData*) + 597
23  libmedCore.dylib              	0x00000001082c0c47 medAbstractData::generateThumbnail() + 151
24  libmedCore.dylib              	0x00000001082cd38f 0x1081d4000 + 1020815
25  QtCore                        	0x0000000107e52c41 QObject::event(QEvent*) + 1073
26  QtGui                         	0x0000000106f239dd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189
27  QtGui                         	0x0000000106f2833e QApplication::notify(QObject*, QEvent*) + 2030
28  QtCore                        	0x0000000107e3e46c QCoreApplication::notifyInternal(QObject*, QEvent*) + 124
29  QtCore                        	0x0000000107e3fa20 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 736
30  com.apple.CoreFoundation      	0x00007fff8a9077e1 CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION + 17
31  com.apple.CoreFoundation      	0x00007fff8a8e6f1c __CFRunLoopDoSources0 + 556
32  com.apple.CoreFoundation      	0x00007fff8a8e643f __CFRunLoopRun + 927
33  com.apple.CoreFoundation      	0x00007fff8a8e5e38 CFRunLoopRunSpecific + 296
34  com.apple.HIToolbox           	0x00007fff94eaa935 RunCurrentEventLoopInMode + 235
35  com.apple.HIToolbox           	0x00007fff94eaa76f ReceiveNextEventCommon + 432
36  com.apple.HIToolbox           	0x00007fff94eaa5af _BlockUntilNextEventMatchingListInModeWithFilter + 71
37  com.apple.AppKit              	0x00007fff8533edf6 _DPSNextEvent + 1067
38  com.apple.AppKit              	0x00007fff8533e226 -[NSApplication _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 454
39  com.apple.AppKit              	0x00007fff85332d80 -[NSApplication run] + 682
40  QtGui                         	0x0000000106edb967 QDesktopWidget::resizeEvent(QResizeEvent*) + 14167
41  QtCore                        	0x0000000107e3d384 QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 68
42  QtCore                        	0x0000000107e3d734 QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) + 324
43  QtCore                        	0x0000000107e3ffac QCoreApplication::exec() + 188
44                                	0x0000000104d73c35 main + 6773
45  libdyld.dylib                 	0x00007fff8e80a5ad start + 1
Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0   libsystem_kernel.dylib        	0x00007fff8bb9eefa kevent_qos + 10
1   libdispatch.dylib             	0x00007fff8d957165 _dispatch_mgr_invoke + 216
2   libdispatch.dylib             	0x00007fff8d956dcd _dispatch_mgr_thread + 52
Thread 2:
0   libsystem_kernel.dylib        	0x00007fff8bb9e5e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff8d9ea578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff8d9e8341 start_wqthread + 13
Thread 3:
0   libsystem_kernel.dylib        	0x00007fff8bb9e5e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff8d9ea578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff8d9e8341 start_wqthread + 13
Thread 4:: com.apple.CFSocket.private
0   libsystem_kernel.dylib        	0x00007fff8bb9e07a __select + 10
1   com.apple.CoreFoundation      	0x00007fff8a92445a __CFSocketManager + 762
2   libsystem_pthread.dylib       	0x00007fff8d9ea99d _pthread_body + 131
3   libsystem_pthread.dylib       	0x00007fff8d9ea91a _pthread_start + 168
4   libsystem_pthread.dylib       	0x00007fff8d9e8351 thread_start + 13
Thread 5:: com.apple.NSEventThread
0   libsystem_kernel.dylib        	0x00007fff8bb97f72 mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff8bb973b3 mach_msg + 55
2   com.apple.CoreFoundation      	0x00007fff8a8e7124 __CFRunLoopServiceMachPort + 212
3   com.apple.CoreFoundation      	0x00007fff8a8e65ec __CFRunLoopRun + 1356
4   com.apple.CoreFoundation      	0x00007fff8a8e5e38 CFRunLoopRunSpecific + 296
5   com.apple.AppKit              	0x00007fff85494d95 _NSEventThread + 149
6   libsystem_pthread.dylib       	0x00007fff8d9ea99d _pthread_body + 131
7   libsystem_pthread.dylib       	0x00007fff8d9ea91a _pthread_start + 168
8   libsystem_pthread.dylib       	0x00007fff8d9e8351 thread_start + 13
Thread 6:: QFileInfoGatherer
0   libsystem_kernel.dylib        	0x00007fff8bb9ddb6 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff8d9eb728 _pthread_cond_wait + 767
2   QtCore                        	0x0000000107d24cd0 QWaitCondition::wait(QMutex*, unsigned long) + 304
3   QtGui                         	0x0000000107418853 QFileSystemModel::sort(int, Qt::SortOrder) + 32499
4   QtCore                        	0x0000000107d24794 QThread::start(QThread::Priority) + 1668
5   libsystem_pthread.dylib       	0x00007fff8d9ea99d _pthread_body + 131
6   libsystem_pthread.dylib       	0x00007fff8d9ea91a _pthread_start + 168
7   libsystem_pthread.dylib       	0x00007fff8d9e8351 thread_start + 13
Thread 7:: QKqueueFileSystemWatcherEngine
0   libsystem_kernel.dylib        	0x00007fff8bb9eeca kevent + 10
1   QtCore                        	0x0000000107e1fbc9 QProcessEnvironment::systemEnvironment() + 55753
2   QtCore                        	0x0000000107d24794 QThread::start(QThread::Priority) + 1668
3   libsystem_pthread.dylib       	0x00007fff8d9ea99d _pthread_body + 131
4   libsystem_pthread.dylib       	0x00007fff8d9ea91a _pthread_start + 168
5   libsystem_pthread.dylib       	0x00007fff8d9e8351 thread_start + 13
Thread 8:
0   libsystem_kernel.dylib        	0x00007fff8bb9e5e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff8d9ea578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff8d9e8341 start_wqthread + 13
Thread 9:: Thread (pooled)
0   libsystem_kernel.dylib        	0x00007fff8bb9ddb6 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff8d9eb728 _pthread_cond_wait + 767
2   QtCore                        	0x0000000107d24cd0 QWaitCondition::wait(QMutex*, unsigned long) + 304
3   QtCore                        	0x0000000107d20386 QSemaphore::acquire(int) + 134
4   QtCore                        	0x0000000107e480a5 QMetaMethod::invoke(QObject*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) const + 1109
5   QtCore                        	0x0000000107e4a70c QMetaObject::invokeMethod(QObject*, char const*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) + 1324
6   libmedCore.dylib              	0x00000001082c0b62 medAbstractData::thumbnail() + 402
7   libmedCore.dylib              	0x000000010827c6a6 medAbstractDatabaseImporter::generateThumbnails(medAbstractData*, QString) + 934
8   libmedCore.dylib              	0x000000010828efa8 medDatabaseImporter::populateDatabaseAndGenerateThumbnails(medAbstractData*, QString) + 88
9   libmedCore.dylib              	0x00000001082734cd medAbstractDatabaseImporter::importFile() + 9021
10  libmedCore.dylib              	0x00000001082710bd medAbstractDatabaseImporter::internalRun() + 109
11  libmedCore.dylib              	0x00000001082c76cb non-virtual thunk to medJobItem::run() + 27
12  QtCore                        	0x0000000107d16a8d QThreadPool::activeThreadCount() const + 1117
13  QtCore                        	0x0000000107d24794 QThread::start(QThread::Priority) + 1668
14  libsystem_pthread.dylib       	0x00007fff8d9ea99d _pthread_body + 131
15  libsystem_pthread.dylib       	0x00007fff8d9ea91a _pthread_start + 168
16  libsystem_pthread.dylib       	0x00007fff8d9e8351 thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x00007f9eb4b05400  rbx: 0x0000000000000002  rcx: 0x00007f9eb33640e0  rdx: 0x00000000000015aa
rdi: 0x00007f9eb3586d10  rsi: 0x00007f9eb2a3cba0  rbp: 0x00007fff5ae91dc0  rsp: 0x00007fff5ae91b30
r8: 0x0000000000000003   r9: 0x0000000000000003  r10: 0x0000000110657501  r11: 0x00000001103fb600
r12: 0x00007f9eb51c42d0  r13: 0x00000000fff7af2f  r14: 0x0000000000000016  r15: 0x00007f9eb3364050
rip: 0x000000010f5c91ef  rfl: 0x0000000000010297  cr2: 0x00007fa6b46dcd78
Logical CPU:     2
Error Code:      0x00000004
Trap Number:     14
Binary Images:
0x104d6b000 -        0x104f0bfff + (??? - ???)  /Applications/MUSIC.app/Contents/MacOS/MUSIC
0x104f44000 -        0x105027fff +QtOpenGL (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL
0x105059000 -        0x1053edfe7 +QtDeclarative (4.8.7) <5A748917-4508-8007-DCBC-2C6542474009> /Applications/MUSIC.app/Contents/Frameworks/QtDeclarative.framework/Versions/4/QtDeclarative
0x105495000 -        0x105510fe7 +QtHelp (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtHelp.framework/Versions/4/QtHelp
0x105539000 -        0x106b1ffe7 +QtWebKit (4.9.4)  /Applications/MUSIC.app/Contents/Frameworks/QtWebKit.framework/Versions/4/QtWebKit
0x106e98000 -        0x1078c9ff7 +QtGui (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtGui.framework/Versions/4/QtGui
0x107ab0000 -        0x107ad3ff7 +QtTest (4.8.7) <55E05A33-5131-EFB9-1129-959BDC964A2D> /Applications/MUSIC.app/Contents/Frameworks/QtTest.framework/Versions/4/QtTest
0x107ade000 -        0x107b1dfef +QtXml (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtXml.framework/Versions/4/QtXml
0x107b34000 -        0x107b6bff7 +QtSql (4.8.7) <90A495CB-2947-5816-EE55-D7B34194B9FE> /Applications/MUSIC.app/Contents/Frameworks/QtSql.framework/Versions/4/QtSql
0x107b7f000 -        0x107cc2fff +QtNetwork (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtNetwork.framework/Versions/4/QtNetwork
0x107cfc000 -        0x107fd6fff +QtCore (4.8.7) <1587CD48-DAD6-622D-3DCA-AF93CD2D02FC> /Applications/MUSIC.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore
0x108047000 -        0x1080a1ff7 +libdtkCore.dylib (0) <22671FDE-AD7A-3B45-98C1-432A13D84658> /Applications/MUSIC.app/Contents/Frameworks/libdtkCore.dylib
0x1080bd000 -        0x1080c1fff +libdtkScript.dylib (0) <87EC016E-9873-3849-B22E-90FA663F9AEB> /Applications/MUSIC.app/Contents/Frameworks/libdtkScript.dylib
0x1080c8000 -        0x108149fff +libdtkGui.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libdtkGui.dylib
0x10817f000 -        0x108199ff7 +libdtkVr.dylib (0) <2860F82A-33EE-3A95-9D87-9B1BC0D03722> /Applications/MUSIC.app/Contents/Frameworks/libdtkVr.dylib
0x1081a3000 -        0x1081a4fff +libdcmtls.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libdcmtls.dylib
0x1081a6000 -        0x1081c1fff +libmedPacs.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libmedPacs.dylib
0x1081d4000 -        0x108348fff +libmedCore.dylib (0) <81BF066D-FF3B-393E-A30B-E8FE343C85C9> /Applications/MUSIC.app/Contents/Frameworks/libmedCore.dylib
0x1083ed000 -        0x1083f1fff  com.apple.agl (3.3.1 - AGL-3.3.1) <11FD7720-F5AC-3719-9CE7-FF8EBDF52B42> /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x1083f9000 -        0x1083faff7 +libitkvcl-4.9.1.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libitkvcl-4.9.1.dylib
0x108400000 -        0x108410ff7 +libdtkLog.dylib (0) <9AF5BECF-394D-3B7D-9D88-B8A9F4C0D266> /Applications/MUSIC.app/Contents/Frameworks/libdtkLog.dylib
0x108423000 -        0x10867bfef +QtScript (4.8.7) <3AC62DCE-CF20-5760-A153-F13C064F6D6E> /Applications/MUSIC.app/Contents/Frameworks/QtScript.framework/Versions/4/QtScript
0x1086d4000 -        0x108724fef +QtSvg (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtSvg.framework/Versions/4/QtSvg
0x108740000 -        0x108befff7 +QtXmlPatterns (4.8.7)  /Applications/MUSIC.app/Contents/Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns
0x108c74000 -        0x108d6eff7 +libQtCLucene.4.dylib (4.8.7) <4CFD739F-DE78-7F81-21FD-F379926D1FF0> /Applications/MUSIC.app/Contents/Frameworks/libQtCLucene.4.dylib
0x108da8000 -        0x108dacfff +libdtkMath.dylib (0) <8EAE8C49-038B-3750-8EB0-63C9E014C715> /Applications/MUSIC.app/Contents/Frameworks/libdtkMath.dylib
0x109073000 -        0x10908efff  com.apple.security.csparser (3.0 - 57337.60.2.1.2)  /System/Library/Frameworks/Security.framework/PlugIns/csparser.bundle/Contents/MacOS/csparser
0x1090a2000 -        0x109147fff  ColorSyncDeprecated.dylib (470.3)  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/Resources/ColorSyncDeprecated.dylib
0x10ca5c000 -        0x10ca62ff7 +libqgif.dylib (0) <6564A7DF-8AB3-8EFA-6D88-01758AA543A5> /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqgif.dylib
0x10ca66000 -        0x10ca6cff7 +libqico.dylib (0)  /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqico.dylib
0x10ca71000 -        0x10caacff7 +libqjpeg.dylib (0) <690AC3EE-FEB6-6637-95BA-936E099D6E2E> /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqjpeg.dylib
0x10cab1000 -        0x10cb05fe7 +libqmng.dylib (0) <6C5AEE56-0868-1688-07E9-119DE7DE4D8F> /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqmng.dylib
0x10cb0d000 -        0x10cb11ff7 +libqsvg.dylib (0)  /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqsvg.dylib
0x10cb16000 -        0x10cb1afff +libqtga.dylib (0) <9DE24A98-3584-C61E-9D16-F1C4664E3408> /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqtga.dylib
0x10cb1e000 -        0x10cb80fff +libqtiff.dylib (0) <2F7A5C7C-7C38-1771-45D6-E36834D07342> /Applications/MUSIC.app/Contents/PlugIns/imageformats/libqtiff.dylib
0x10cc29000 -        0x10ccaffef +libqsqlite.dylib (0) <9034199E-D2B8-BC3D-3574-3C9507E6BE4E> /Applications/MUSIC.app/Contents/PlugIns/sqldrivers/libqsqlite.dylib
0x10e2ce000 -        0x10e2e8ff7 +libcartoNavxReadersWritersPlugin.dylib (0) <2C860342-0616-348B-AA26-CC41C9A2DB4F> /Applications/MUSIC.app/Contents/PlugIns/libcartoNavxReadersWritersPlugin.dylib
0x10e2f4000 -        0x10e430ff7 +libvtkInfovis.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtkInfovis.5.10.dylib
0x10e49d000 -        0x10e7e2fff +libmedVtkInria.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libmedVtkInria.dylib
0x10e8ce000 -        0x10e9b6fff +libvtkWidgets.5.10.dylib (0) <196C139E-AF6A-3167-9275-189D511A4951> /Applications/MUSIC.app/Contents/Frameworks/libvtkWidgets.5.10.dylib
0x10ea32000 -        0x10ebb6fff +libvtkHybrid.5.10.dylib (0) <87323EE5-1459-3FC4-B8F9-F82807DDB3B1> /Applications/MUSIC.app/Contents/Frameworks/libvtkHybrid.5.10.dylib
0x10ec45000 -        0x10ef34fff +libvtkVolumeRendering.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtkVolumeRendering.5.10.dylib
0x10f151000 -        0x10f39fff7 +libvtkRendering.5.10.dylib (0) <089F9F55-B970-38BF-9E74-E6E155B3B6F4> /Applications/MUSIC.app/Contents/Frameworks/libvtkRendering.5.10.dylib
0x10f537000 -        0x10fa83fff +libvtkGraphics.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtkGraphics.5.10.dylib
0x10fbab000 -        0x10fe3afff +libvtkImaging.5.10.dylib (0) <842BB100-4A70-3984-A6FF-08F396A671FE> /Applications/MUSIC.app/Contents/Frameworks/libvtkImaging.5.10.dylib
0x10fece000 -        0x1102b9fff +libvtkIO.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtkIO.5.10.dylib
0x1103a3000 -        0x110616fff +libvtkFiltering.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtkFiltering.5.10.dylib
0x1106ff000 -        0x110949fff +libvtkCommon.5.10.dylib (0) <4973A965-AF9F-35A0-A246-D3891043B261> /Applications/MUSIC.app/Contents/Frameworks/libvtkCommon.5.10.dylib
0x110a0b000 -        0x110a33fff +libvtksys.5.10.dylib (0) <59CE0F80-AF11-34DD-BD86-25ADAB1779C4> /Applications/MUSIC.app/Contents/Frameworks/libvtksys.5.10.dylib
0x110a46000 -        0x110b7efff +libvtklibxml2.5.10.dylib (0)  /Applications/MUSIC.app/Contents/Frameworks/libvtklibxml2.5.10.dylib
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External Modification Summary:
Calls made by other processes targeting this process:
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Calls made by this process:
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thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 4557
thread_create: 0
thread_set_state: 0
VM Region Summary:
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Writable regions: Total=175.9M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=175.9M(100%)
                            VIRTUAL   REGION

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===========                     =======  =======
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===========                     =======  =======
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I dont know about the heavy data but for sure MUSIC doesn't read unstructured grid data which is the type of seg_cropped that why it crashed

authors: mathildemerle msermesant paulineMig

repo: Inria-Asclepios/medInria-public


text:
BUG: Fix MatrixOffsetTransformBase SetFixedParameters if too few params

When a user provided too few parameters as argument to
MatrixOffsetTransformBase::SetFixedParameters, the member function
would have undefined behavior, which would typically just cause a crash.
This issue affects transforms derived from MatrixOffsetTransformBase, including:
AffineTransform
AzimuthElevationToCartesianTransform
CenteredAffineTransform
Euler2DTransform
FixedCenterOfRotationAffineTransform
QuaternionRigidTransform
Rigid2DTransform
Rigid3DTransform
ScalableAffineTransform
ScaleLogarithmicTransform
ScaleSkewVersor3DTransform
ScaleTransform
ScaleVersor3DTransform
Similarity2DTransform
Similarity3DTransform
VersorRigid3DTransform
VersorTransform

A crash could occur when reading a transform from a transform file, when
this file has an insufficient number of fixed parameters. It was
encountered when loading a transform within 3DSlicer (version
4.11.20200930).
The fix consists of throwing an exception when the number of fixed
parameters is too small.

Sorry to chime in. Thanks for doing this @N-Dekker :100:. Can the condition be tested, e.g. by adding the file that triggered the crash and the corresponding code in the appropriate class test, or by adding a case where a faulty parameter file is simulated by appropriately removing parameters or dimensions for an existing parameter file in the class' test file?

Can the condition be tested, e.g. by adding the file that triggered the crash and the corresponding code in the appropriate class test, or by adding a case where a faulty parameter file is simulated by appropriately removing parameters or dimensions for an existing parameter file in the class' test file?

@jhlegarreta  Thanks for your suggestion, Jon. I agree that a test would be helpful. Actually I'm thinking now of adding a low-level unit test, that directly calls SetFixedParameters with an insufficient number of fixed-parameters. Hope that's OK to you as well.
In the mean-time, it would be helpful if you could confirm the issue by loading such a file yourself, for example:
#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
FixedParameters:

(Note: FixedParameters intentionally left blank!)
For example, using 3D Slicer. Are you able to reproduce the application crash?

Actually I'm thinking now of adding a low-level unit test, that directly calls SetFixedParameters with an insufficient number of fixed-parameters. Hope that's OK to you as well.

Sounds good. Thanks Niels.

In the mean-time, it would be helpful if you could confirm the issue by loading such a file yourself, for example: For example, using 3D Slicer. Are you able to reproduce the application crash?

Sorry Niels, but I will not be able to do this; I do not use 3D Slicer as of today, and I prefer not to start that front on my machine for a few reasons. I do believe the issue exists; I just made the comment because I believe that testing and ensuring that the condition is working is also important. I am well aware that it requires an additional effort, but one that is worthwhile.

Another possible approach could be to allow an empty FixedParameters argument to specify that the fixed parameters are all zero. MatrixOffsetTransformBase::SetFixedParameters would then set m_Center to zero (the origin). Would anyone here like that better than just throwing an exception?

empty FixedParameters

How many Slicer-written files with no fixed parameters are there? If many, we could make a special case that empty means all zeroes. If not many, I prefer we throw. Specifying all zeroes is easy enough.

@lassoan Hi Andras, could you also please have a look at this pull request? Do you agree that it might indeed fix a potential 3D Slicer crash (when the user provides a transform file that does not have enough FixedParameters).

could you also please have a look at this pull request? Do you agree that it might indeed fix a potential 3D Slicer crash (when the user provides a transform file that does not have enough FixedParameters).

The change looks good to me. It indeed caused problem in Slicer (it caused some exception that was captured at some level, but left the application in an inconsistent state). I've tested this proposed fix and it makes loading fail with a nice descriptive error message.
It would be nice to replace the plain text transform file format with a simple json-based format (and json schema to clearly specify what parts of the file are optional and describe the meaning of the parameters).

How many Slicer-written files with no fixed parameters are there?

@dzenanz I guess Slicer-written transform files always have the correct number of fixed parameters, but Andras @lassoan please correct me if I'm wrong!
But allowing an empty FixedParameters does ease manually editing a transform file. Which is what I did, when trying to load a transform file from elastix into 3DSlicer (as part of pull request https://github.com/SuperElastix/elastix/pull/358).

Specifying all zeroes is easy enough.

It was not directly obvious to me how many zeroes to specify, for a specific transform. It appears dependent on the dimensionality as well as the transformation type. Please look at the table below here! Anyway, the main aim of this pull request is to avoid application crashes. So if you do not like my suggestion to allow an empty list of FixedParameters to specify all zeroes, it would be fine to me to just have the current version of this pull request merged. 😃

Transform type
# FixedParameters

AffineTransform<double,2>
2

AffineTransform<double,3>
3

AffineTransform<double,4>
4

AzimuthElevationToCartesianTransform<double,3>
3

BSplineDeformableTransform<double,2,2>
10

BSplineDeformableTransform<double,3,3>
18

BSplineSmoothingOnUpdateDisplacementFieldTransform<double,2>
10

BSplineSmoothingOnUpdateDisplacementFieldTransform<double,3>
18

BSplineTransform<double,2,3>
10

BSplineTransform<double,3,3>
18

CenteredAffineTransform<double,2>
2

CenteredAffineTransform<double,3>
3

CenteredEuler3DTransform
4

CenteredRigid2DTransform
2

CenteredSimilarity2DTransform
2

CompositeTransform<double,2>
0

CompositeTransform<double,3>
0

CompositeTransform<double,4>
0

ConstantVelocityFieldTransform<double,2>
10

ConstantVelocityFieldTransform<double,3>
18

DisplacementFieldTransform<double,2>
10

DisplacementFieldTransform<double,3>
18

Euler2DTransform
2

Euler3DTransform
4

FixedCenterOfRotationAffineTransform<double,3>
3

GaussianExponentialDiffeomorphicTransform<double,2>
10

GaussianExponentialDiffeomorphicTransform<double,3>
18

GaussianSmoothingOnUpdateDisplacementFieldTransform<double,2>
10

GaussianSmoothingOnUpdateDisplacementFieldTransform<double,3>
18

GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<double,2>
18

GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<double,3>
28

IdentityTransform<double,2>
0

IdentityTransform<double,3>
0

IdentityTransform<double,4>
0

QuaternionRigidTransform
3

Rigid2DTransform
2

Rigid3DPerspectiveTransform
0

v3::Rigid3DTransform
3

ScalableAffineTransform<double,3>
3

ScaleLogarithmicTransform<double,3>
3

ScaleSkewVersor3DTransform
3

ScaleTransform<double,2>
2

ScaleTransform<double,3>
3

ScaleTransform<double,4>
4

ScaleVersor3DTransform
3

Similarity2DTransform
2

Similarity3DTransform
3

TimeVaryingBSplineVelocityFieldTransform<double,2>
18

TimeVaryingBSplineVelocityFieldTransform<double,3>
28

TimeVaryingVelocityFieldTransform<double,2>
18

TimeVaryingVelocityFieldTransform<double,3>
28

TranslationTransform<double,2>
0

TranslationTransform<double,3>
0

TranslationTransform<double,4>
0

VelocityFieldTransform<double,2>
18

VelocityFieldTransform<double,3>
28

VersorRigid3DTransform
3

VersorTransform
3

It was not directly obvious to me how many zeroes to specify

For manual editing, I think adding extra numbers (zeroes) at the end is not a problem.

it would be fine to me to just have the current version of this pull request merged

OK.

Sorry Niels, but I will not be able to do this; I do not use 3D Slicer as of today, and I prefer not to start that front on my machine for a few reasons. I do believe the issue exists; I just made the comment because I believe that testing and ensuring that the condition is working is also important. I am well aware that it requires an additional effort, but one that is worthwhile.

@N-Dekker many thanks for having added a test :medal_sports: and the work in this PR.

Slicer uses ITK to write transforms, so all parameters are expected to written correctly.
SlicerElastix extension provide an interface to Elastix (you can specify a binary Elastix installation or use the bundled Elastix version) and takes care of converting Elastix transforms to ITK transforms (linear, bspline, grid) - see https://github.com/lassoan/SlicerElastix/blob/master/Elastix/Elastix.py#L525-L694.
It would be nice if Elastix would use ITK transform format directly, but I can understand that the plain text file format is not appealing and flexible enough.

SlicerElastix extension provide an interface to Elastix (you can specify a binary Elastix installation or use the bundled Elastix version) and takes care of converting Elastix transforms to ITK transforms (linear, bspline, grid) - see https://github.com/lassoan/SlicerElastix/blob/master/Elastix/Elastix.py#L525-L694.

Very interesting, @lassoan I'm currently trying to figure out if (or when) an elastix transform could be converted to a corresponding ITK transform, within elastix core function TransformBase<TElastix>::WriteToFile: https://github.com/SuperElastix/elastix/pull/358 But as far as I can see, elastix has 17 transform types, and ITK has 58 of them. Not sure if a one-to-one correspondence is always possible.

source: gharchive/pull-request

authors: N-Dekker dzenanz jhlegarreta lassoan

repo: InsightSoftwareConsortium/ITK

license_type: permissive

license_source: github-api


text:
ENH: Test BuildInformation GetValue, GetDescription for an l-value key

Added a check that for each entry from the map retrieved by GetMap(),
both GetValue(key) and GetDescription(key) return the expected
string.

@hjmjohnson Can you possibly recall why these GetValue and GetDescription member functions were declared this way, having a const r-value reference const MapKeyType && as parameter type?  You know, const r-value references are quite rare in C++, as r-value references are mostly used to "move" from, whereas const actually prevents doing such a "move".
It seems to me that an old-style const MapKeyType & (const l-value reference) would be just fine here.
https://github.com/InsightSoftwareConsortium/ITK/blob/a908033cacbbf7d23c12941cb69e39da336c8ee1/Modules/Core/Common/include/itkBuildInformation.h#L86-L87

@dzenanz @hjmjohnson  As this pull request still needs to be adjusted anyway, would you agree that the std::cout statement that prints all map entries may just be removed, once each map entry is checked by those two EXPECT_EQ calls?
https://github.com/InsightSoftwareConsortium/ITK/blob/9a0be4934e7656d8aa4ba98b7d8c6d293ae7074b/Modules/Core/Common/test/itkBuildInformationGTest.cxx#L50-L62

The test seems somewhat tautological. But I guess many tests do. Since no one is probably checking that output, I am fine with removing it.

https://open.cdash.org/viewBuildError.php?buildid=7646720  (Azure.fv-az200-80, Windows_NT-Build7319...) says:

itkBuildInformationGTest.cxx(59): error C2664: 'const itk::BuildInformation::MapValueType itk::BuildInformation::GetValue(const itk::BuildInformation::MapKeyType &&)': cannot convert argument 1 from '_Ty1' to 'const itk::BuildInformation::MapKeyType &&'

https://open.cdash.org/viewBuildError.php?buildid=7646718 (Azure.Mac-1640624256914, Darwin-Build7268...) says:

itkBuildInformationGTest.cxx:59:47: error: rvalue reference to type 'const basic_string<...>' cannot bind to lvalue of type 'const basic_string<...>'

https://open.cdash.org/viewBuildError.php?buildid=7646711  (Azure.fv-az36-134, Linux-Build7338...) says:

itkBuildInformationGTest.cxx:59:50: error: cannot bind rvalue reference of type 'const MapKeyType&& {aka const std::__cxx11::basic_string&&}' to lvalue of type 'const std::__cxx11::basic_string'

@hjmjohnson @dzenanz Do you agree that the signatures of GetValue(const MapKeyType &&) and GetDescription(const MapKeyType &&) should just have a single &?

I don't think that itk::BuildInformation is a widely used class. You are one of the rare people who even looked at it. You want to show it some love? Sure, go ahead. I am fine with changes to this class, as long as everything compiles 😄

@hjmjohnson Can you possibly recall why these GetValue and GetDescription member functions were declared this way, having a const r-value reference const MapKeyType && as parameter type? You know, const r-value references are quite rare in C++, as r-value references are mostly used to "move" from, whereas const actually prevents doing such a "move".
It seems to me that an old-style const MapKeyType & (const l-value reference) would be just fine here.
https://github.com/InsightSoftwareConsortium/ITK/blob/a908033cacbbf7d23c12941cb69e39da336c8ee1/Modules/Core/Common/include/itkBuildInformation.h#L86-L87

I probably made a mistake here.  A change would be welcomed.

authors: N-Dekker dzenanz hjmjohnson


text:
COMP: Use GNU tar and extract only relevant files

Fixes the following error:
./macpython-download-cache-and-build-module-wheels.sh: line 81: /Users/svc-dashboard/D/P/ITKPythonPackage/scripts/macpython-install-python.sh: No such file or directory Building module wheels
./macpython-download-cache-and-build-module-wheels.sh: line 85: /Users/svc-dashboard/D/P/ITKPythonPackage/scripts/macpython-build-module-wheels.sh: No such file or directory

👍

authors: dzenanz thewtex