[Hugo]

No @outtt

The m_mapper variable l.94 in ROIBarycentricMapping.inl is used but not declared in your code. Where does it come from?

Hugo

[Hugo]

Hi @charles

You are talking about a 2006 paper! I was even not done with my studies!

I don’t see the appropriate equations that you mention. Can you indicate me using the linked paper above?

A more recent paper is available here: Interactive simulation of embolization coils: Modeling and experimental validation

Again, this corresponds to the “Catheter and coil simulation” item described online.

Best

Hugo

[Hugo]

Hi @outtt

I got the following error compiling your code:

 error: type 'int' cannot be used prior to '::' because it has no members
    typedef typename T::SPtr SPtr;
                     ^
In file included from ../ROIBarycentricMapping.cpp:2:
../ROIBarycentricMapping.inl:94:4: error: use of undeclared identifier 'm_mapper'
                        m_mapper = m;
                        ^
../ROIBarycentricMapping.inl:117:6: error: use of undeclared identifier 'm_mapper'
        if (m_mapper)
            ^
../ROIBarycentricMapping.inl:119:3: error: use of undeclared identifier 'm_mapper'
                m_mapper->setName("mapper");
                ^
../ROIBarycentricMapping.inl:120:18: error: use of undeclared identifier 'm_mapper'
                this->addSlave(m_mapper.get());
                               ^
../ROIBarycentricMapping.inl:121:3: error: use of undeclared identifier 'm_mapper'
                m_mapper->maskFrom = this->maskFrom;
                ^
../ROIBarycentricMapping.inl:122:3: error: use of undeclared identifier 'm_mapper'
                m_mapper->maskTo = this->maskTo;
                ^
../ROIBarycentricMapping.inl:129:2: error: use of undeclared identifier 'topology_from'
        topology_from = this->fromModel->getContext()->getMeshTopology();
        ^
../ROIBarycentricMapping.inl:130:2: error: use of undeclared identifier 'topology_to'
        topology_to = this->toModel->getContext()->getMeshTopology();
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]

Note also that your CMakeLists.txt needs changes to be compiled externally from SOFA:

cmake_minimum_required(VERSION 2.8.12)

project(ROIBarycentricMapping)

find_package(SofaFramework REQUIRED)
find_package(SofaBase REQUIRED)
find_package(SofaGeneral REQUIRED)

set(HEADER_FILES
      initPlugin.h
      ROIBarycentricMapping.h
      ROIBarycentricMapping.inl
)

set(SOURCE_FILES
      initPlugin.cpp
      ROIBarycentricMapping.cpp
)

add_library(${PROJECT_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES} ${SCENES_FILES} ${README_FILES})
set_target_properties(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "-DPLUGIN_DATA_DIR=\"${CMAKE_CURRENT_SOURCE_DIR}/\"")
set_target_properties(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "-DSOFA_BUILD_ROIBARYCENTRICMAPPING")
target_link_libraries(${PROJECT_NAME} SofaCore SofaHelper SofaUserInteraction SofaBaseMechanics SofaEigen2Solver)
include_directories("${CMAKE_CURRENT_SOURCE_DIR}/..")

install(TARGETS ${PROJECT_NAME}
        COMPONENT ROIBarycentricMapping_libraries
        EXPORT ROIBarycentricMappingTargets
        RUNTIME DESTINATION bin
        LIBRARY DESTINATION lib
        ARCHIVE DESTINATION lib)

Cheers

Hugo

[Hugo]

Hi @ma1991

No dumb question here.
When things are misunderstood, it means it can be better explained.

You can actually load or export both STL and VTK. So the transformation of one into the other should be not prob.

Hugo

[Hugo]

Hi @ma1991

You have two options: you can either export at begin (exportAtBegin=”1″) or at end (exportAtEnd=”1″)

Note that obj are surface-only format, while vtk is a format for both surface and volume meshed.

Best wishes

Hugo

[Hugo]

It seems your BoxROI is huge compared to your object.
Moreover it appears that the box is not including any part (i.e. any indice) of your mesh.

Hugo

[Hugo]

Hi @charles,

You can specify to your MechanicalObject (containing the rigid frames) their position and orientation with a quaternion.
I think the ArticulatedSystemMapping is close to what you need but I remember struggling a bit myself using it, but it’s worth having a look (in examples/Components/mapping)

Best

Hugo

[Hugo]

Hi @ma1991

Thank you very much for sharing your objectives. It definitely helps our understanding.

Best,

Hugo

[Hugo]

Hi Marwa,

I don’t really understand your issue.
You want to apply a FixedConstraint on your mesh in the simulation, is this what you want ?
Your piece of code is showing the creation of a BoxROI, which is done properly.

Best

Hugo

[Hugo]

Hi @lucaam86 and welcome on the SOFA forum!

First of all, thank you very much for making the effort of generating a video and sharing your scene with us. It helps.
Could you also share the mesh with us? if not, could you at least send it to me only so that I can test it.

I can already tell you that the issue might come from the numerical parameters that you set (dimensions, stiffness/mass, timestep)/

Best wishes,

Hugo

[Hugo]

Hi Marwa @ma1991

Indeed, your vtu mesh is only a surface and do not include any volumetric element (no tetrahedron). Have a look at the screenshot (crop in the volume of the mesh, only the surface appears):

Best

Hugo

[Hugo]

Hi @charles

Yes I do.
How can I help? Would you be interested in getting access to the related simulation code?

If so, you can contact me directly by clicking on “Get This Plugin” on the associated Marketplace item.

Best wishes,

Hugo

[Hugo]

Hi @ma1991

Here the error is clear: the TetrahedronFEMForceField can not work properly without a tetrahedral topology on which to compute the integration of the linear elasticitic constitutive law.

Could you share the generated VTK mesh? I would guess that something went wrong with your meshing step.

Best,

Hugo

[Hugo]

Hi Noura,

is in charge of the continuous integration (CI), he will confirm what I write.
But the options are actually defined in the CI scripts, more precisely in the configure.sh

Let me know if it helps.

Hugo

[Hugo]

Hi @pguillon

I think what you want to do is to fill the MechanicalObject with the field position containing the deformed positions and the field rest_position with the undeformed positions. However, the internal forces computation might depend from the code you are using. Which FEM constitutive model are you using?

Hugo

[Hugo]

Hi @agniv

The first concern that I have is that you are mixing two notions of “nodes”.
I would rather name the indices that you want to pass to your constraint: self.constraintIndices

Because node is also the graph node..

The idea of looking into the force vector was good, I don’t know exactly what makes the values to suddenly jump..
Internal forces resulting from imposed displacement are computed by the mechanical constitutive law. Depending on the FEM mechanical model you are using, you could export in the C++ code the vector resulting from the addForce() function.

Best

Hugo

[Hugo]

Hi @ma1991

Are you sure of your path?
could you also try doing filename=str(path)+’bunny0.vtu’ ?

[ERROR] [MeshVTKLoader] Error while parsing XML
this sounds like something wrong is passed as argument to the MeshVTKLoader and can not be parsed.

Best

Hugo

[Hugo]

Hi @charles

I am really sorry for the delay of my reply to your private email. I answered it. We are currently very busy focused on the SOFA Week.

Prices can not be directly provided since authors / institutions owning the codes have different practices. Moreover, prices depend on many parameters like use, domain of use, exclusivity etc.

Let’s continue this discussion per email and I will provide you all appropriate contacts and information.

Best wishes,

Hugo

[Hugo]

Hi @shuo

Let me poke Lekan with the correct forum nickname.

@lakehanne Hitss needs you help. Could you share us how you solved the problem?

Best

Hugo

[Hugo]

Hi @ma1991

What was the hotkey on Linux ?

Hugo

[Hugo]

Hi @pguillon

If I understand correctly, you want to load the two configuration:
– the rest volumetric mesh
– the deformed surface mesh
and use a MeshSpringForceField to fit both and recover the stressed configuration.

Is this what you target?

Hugo

[Hugo]

Hi @outtt

You can share with us the simulation case you would like to accelerate. I could give a look at it. I could also give a try using the MOR plugin.

You know that this plugin freshly comes from research and is made open-source. Documentation and support is unfortunately time consuming and researchers dedicate themself on their spare time.

I am willing to help you, let me know how.

Hugo

[Hugo]

Hi @pguillon

Was the approach described in the scene ICPRegistration_MeshSpring.scn fitting your needs though?

You could also have a look at another example: examples/Components/constraint/AffineMovementConstraint.scn

Hugo

[Hugo]

Hi @fleonard

To work with the approach involving the RestShapeSpringForceField, you could simply pass these rest positions to the MechanicalObject at the init (from a loader) like :

<MeshObjLoader name="undeformed" filename="mesh1.obj"/>
<MeshObjLoader name="deformed-targetConfiguration" filename="mesh2.obj"/>
<MechanicalObject name="Dofs" position="@undeformed.position" rest_position="@deformed-targetConfiguration.position" />
<RestShapeSpringForceField />

Best,

Hugo

[Hugo]

Hi @outtt

I can understand it is hard in the first steps to use a new plugin. You can maybe try to create an issue on the associated GitHub if it’s dev questions. If it is user question, you can post them here. I would poke the authors.

Indeed, coming to the SOFA Week is the perfect time for this. Are you sure not to be able to join us?

Best

Hugo

[Author]

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