Tearing simulation with Sofapython

[SalemTree]

I'm trying to make a simulation of capsulorhexis which is an eye surgery operation of tearing a part on the lens capsule.
I have checked previous posts like https://www.sofa-framework.org/community/forum/topic/simulation-of-tearing-a-part-on-the-lens-capsule/ or plugin like SofaTearing,
The effect I'm trying to achieve is as following link:
https://github.com/alireza-montazeri/SofaTearing/blob/master/example/test.gif

Unfortunately I'm having some problems with methods in the other posts and I'm not familiar with c++, could you enlighten a way that I can acchieve this kind of simulation with SofaPython? Thank you so much.

[SalemTree]

@hugtalbot Hi, Hugo, Sorry to bother but could you share some thoughts on this subject please?

[hugh-min]

Hi @epernod ,
My sofa version is 21.12, I think it might be the way I'm installing the plugin, i cloned the tearing project into a 'ext_plugin_repo' directory and tried to build it from cmake, is this the right way to do it?

[epernod]

Hi,
this method should work as it the workflow used on github action here: https://github.com/InfinyTech3D/Tearing/releases
Otherwise are you compiling SOFA from the source? You can add it to your list of external plugin and compile it inside SOFA.

[hugtalbot]

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[hugh-min]

@epernod
Thanks！I switched to compiled version of SOFA and it works.
The tearing plugin is incredible and I think this is the function i need.
In the SquareTissue scenes i encounter unpected crash when interacting with the cloth by holding SHIFT and pulling it.
I'm using compiled SOFA on windows and I get following message in prompt window after the crash

########## SIG 22 - SIGABRT: usually caused by an abort() or assert() ##########
  sofa::helper::BackTrace::dump
  sofa::helper::BackTrace::sig
  raise
  abort
  purecall
  sofa::helper::logging::MessageDispatcher::process
  sofa::helper::logging::MessageDispatcher::LoggerStream::~LoggerStream
  sofa::helper::printLibraryNotCleanedUpWarning
  sofa::core::visual::VisualParams::zFar
  execute_onexit_table
  execute_onexit_table
  execute_onexit_table
  sofa::core::visual::VisualParams::defaultInstance
  sofa::core::visual::VisualParams::defaultInstance
  RtlActivateActivationContextUnsafeFast
  LdrShutdownProcess
  RtlExitUserProcess
  ExitProcess
  rand_s
  raise
  sofa::helper::BackTrace::sig
  seh_filter_exe
  seh_filter_exe
  _C_specific_handler
  _chkstk
  RtlGetExtendedContextLength2
  KiUserExceptionDispatcher
  sofa::component::topology::container::dynamic::PointSetTopologyContainer::setPointTopologyToDirty
  sofa::component::topology::container::dynamic::PointSetTopologyModifier::addPointsWarning
  sofa::component::topology::container::dynamic::PointSetTopologyModifier::addPoints
  sofa::component::topology::container::dynamic::TriangleSetGeometryAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3,double>,sofa::type::Vec<3,double>,double> >::SplitAlongPath
  sofa::component::TearingAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3,double>,sofa::type::Vec<3,double>,double> >::splitting
  sofa::component::TearingAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3,double>,sofa::type::Vec<3,double>,double> >::algoFracturePath
  sofa::component::engine::TearingEngine<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3,double>,sofa::type::Vec<3,double>,double> >::algoFracturePath
  sofa::component::engine::TearingEngine<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3,double>,sofa::type::Vec<3,double>,double> >::handleEvent
  sofa::simulation::PropagateEventVisitor::processObject
  sofa::simulation::PrintVisitor::treeTraversal
  sofa::simulation::PrintVisitor::treeTraversal
  sofa::simulation::PropagateEventVisitor::processNodeTopDown
  sofa::simulation::graph::DAGNode::executeVisitorTopDown
  sofa::simulation::graph::DAGNode::executeVisitorTopDown
  sofa::simulation::graph::DAGNode::doExecuteVisitor
  sofa::simulation::Node::executeVisitor
  sofa::simulation::DefaultAnimationLoop::step
  sofa::simulation::Simulation::animate
  sofa::gui::qt::RealGUI::step
  QMetaObject::activate
  QTimer::timerEvent
  QObject::event
  QApplicationPrivate::notify_helper
  QApplication::notify
  QCoreApplication::notifyInternal2
  QEventDispatcherWin32::event
  QApplicationPrivate::notify_helper
  QApplication::notify
  QCoreApplication::notifyInternal2
  QCoreApplicationPrivate::sendPostedEvents
  qt_plugin_query_metadata
  QEventDispatcherWin32::processEvents
  GetPropW
  DispatchMessageW
  QEventDispatcherWin32::processEvents
  qt_plugin_query_metadata
  QEventLoop::exec
  QCoreApplication::exec
  sofa::gui::qt::RealGUI::mainLoop
  sofa::gui::common::GUIManager::MainLoop
  sofa::gui::common::GUIManager::MainLoop
  sofa::gui::common::GUIManager::MainLoop
  BaseThreadInitThunk
  RtlUserThreadStart

[epernod]

I think the bug your are mentioning is the same as this one: #3370
Could you confirm it is the same scenario?
Hopefully it has been already solved but only a few days ago. So you will need to use an up to date version to avoid this crash.

[hugh-min]

@epernod
I tried to update to latest SOFA master and now my environment is:
OS: Ubuntu 21.10
SOFA version: v22.12.99
Tearing plugin: Tearing_license_for-SOFA-master_Linux
I still run into crash while running the example scenes such as scenes in TearingEngine
the crash is recorded:

tearing.crash.mp4

one of the error message while running SquareTissue_06_circleHole_pressureBorder.scn is as follows. No keyboard/mouse interaction was made during the simulation:

[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[ERROR]   [TriangleSetGeometryAlgorithms(GeomAlgo)]  Error: SplitAlongPath: vertxInTriangle not found in EDGE::POINT case
[ERROR]   [TriangleSetGeometryAlgorithms(GeomAlgo)] ERROR: in the incision path. 
[ERROR]   [TriangleFEMUtils] Null determinant in computeStrainDisplacementGlobal: 0
[ERROR]   [TriangularFEMForceField(FEM)] Division by zero exception in computeStrainDisplacementLocal
[ERROR]   [TriangleSetGeometryAlgorithms(GeomAlgo)] Cannot split an edge with 3!=2 attached triangles. Around edge: 848
[ERROR]   [TriangleSetGeometryAlgorithms(GeomAlgo)] Which is composed of vertex: 328 330
[ERROR]   [TopologicalChangeManager]  in InciseAlongEdgeList
[ERROR]   [TriangleFEMUtils] Null determinant in computeStrainDisplacementGlobal: 1.02859e-32
[ERROR]   [TriangularFEMForceField(FEM)] Division by zero exception in computeStrainDisplacementLocal

########## SIG 11 - SIGSEGV: segfault ##########
  sofa::helper::BackTrace::sig(int)
  sofa::component::topology::container::dynamic::TriangleSetGeometryAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::SplitAlongPath(unsigned int, sofa::type::Vec<3u, double>&, unsigned int, sofa::type::Vec<3u, double>&, sofa::type::vector<sofa::geometry::ElementType, sofa::type::CPUMemoryManager<sofa::geometry::ElementType> >&, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >&, sofa::type::vector<sofa::type::Vec<3u, double>, sofa::type::CPUMemoryManager<sofa::type::Vec<3u, double> > >&, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >&, double, double)
  sofa::component::TearingAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::splitting(int, int, sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, int, int, sofa::type::vector<sofa::geometry::ElementType, sofa::type::CPUMemoryManager<sofa::geometry::ElementType> >, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >, sofa::type::vector<sofa::type::Vec<3u, double>, sofa::type::CPUMemoryManager<sofa::type::Vec<3u, double> > >, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >&)
  sofa::component::TearingAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::algoFracturePath(sofa::type::Vec<3u, double>, unsigned int, sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, unsigned int, sofa::type::Vec<3u, double>, sofa::type::vector<sofa::type::Vec<3u, double>, sofa::type::CPUMemoryManager<sofa::type::Vec<3u, double> > > const&)
  sofa::component::engine::TearingEngine<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::algoFracturePath()
  sofa::component::engine::TearingEngine<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::handleEvent(sofa::core::objectmodel::Event*)
  sofa::simulation::PropagateEventVisitor::processNodeTopDown(sofa::simulation::Node*)
  sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::graph::DAGNode*> >&, std::map<sofa::simulation::graph::DAGNode*, sofa::simulation::graph::DAGNode::StatusStruct, std::less<sofa::simulation::graph::DAGNode*>, std::allocator<std::pair<sofa::simulation::graph::DAGNode* const, sofa::simulation::graph::DAGNode::StatusStruct> > >&, sofa::simulation::graph::DAGNode*)
  sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::graph::DAGNode*> >&, std::map<sofa::simulation::graph::DAGNode*, sofa::simulation::graph::DAGNode::StatusStruct, std::less<sofa::simulation::graph::DAGNode*>, std::allocator<std::pair<sofa::simulation::graph::DAGNode* const, sofa::simulation::graph::DAGNode::StatusStruct> > >&, sofa::simulation::graph::DAGNode*)
  sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)
  sofa::simulation::DefaultAnimationLoop::step(sofa::core::ExecParams const*, double)
  sofa::simulation::Simulation::animate(sofa::simulation::Node*, double)
  sofa::gui::qt::RealGUI::step()
  QTimer::timeout(QTimer::QPrivateSignal)
  QObject::event(QEvent*)
  QApplicationPrivate::notify_helper(QObject*, QEvent*)
  QCoreApplication::notifyInternal2(QObject*, QEvent*)
  QTimerInfoList::activateTimers()
  g_main_context_dispatch
  g_main_context_iteration
  QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)
  QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)
  QCoreApplication::exec()
  sofa::gui::qt::RealGUI::mainLoop()
  sofa::gui::common::GUIManager::MainLoop(boost::intrusive_ptr<sofa::simulation::Node>, char const*)
  __libc_start_main
Segmentation fault (core dumped)

[epernod]

Hi, Sorry for the late reply.
Are you compiling SOFA on your own or using binaries?
From what I see, you are using the master branch, do you know how old is your version ?
I have been fixing bugs related to topology in the core of SOFA in the last months so I suggest to make sure you are using a recent version of SOFA.

[hugh-min]

@epernod
I compiled SOFA on my own but did not compiled the tearing plugin, I imported the plugin through the plugin manager.
This is the git info inside the plugin branch:

# Git info for Tearing

## Current commit
## git rev-parse --abbrev-ref HEAD
aa470c618ccf37a1fe60f617b99597e4c8acfad5

## Branches containing current commit
## git branch -a --contains aa470c618ccf37a1fe60f617b99597e4c8acfad5 

I pulled the lastest release of the plugin last week just before i posted about the crash, so I presume it's an up-to-date one.

[epernod]

Sorry I meant, which git revision of SOFA

[hugh-min]

the git revision of SOFA in the video is a5e65ab
I also tried the plugin on v22.06 version of SOFA and the error was the same.

[hugtalbot]

@SalemTree @hugh-min have you tried with the latest version of https://github.com/InfinyTech3D/Tearing ?

[github-actions[bot]]

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@SalemTree
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[github-actions[bot]]

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@SalemTree
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[github-actions[bot]]

⚠️ ⚠️ ⚠️
@SalemTree
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.