[SOLVED] sample code

[SdAuto]

Hello,
i am new to SOFA, i ask you please, is it possible to modify the code of liver for take a piece of soft tissue? if it is, please can you give me an example of liver.
thank you for all your help

[Hugo]

Dear SdAuto,

Could you please detail what you mean by “modify the code of liver for take a piece of soft tissue”?
If you download the binaries of SOFA, you will be able to run examples as the one in examples/Demos/liver.scn

Cheers,

Hugo

[SdAuto]

Hi sir,

I already saw the example but i want to know if i can remove a part of the liver for examination, or make a wound and suture it.

Thank you sir

[Hugo]

Hi,

If what you want to do is cutting during the simulation, you can:

• have a look to the examples in examples/Components/topology/TopologicalModifiers
• look at all the threads about cutting and topological changes on the forum like:
  • Incise without mouse
  • how to incise 3d object

If what you need is just to edit a mesh, you should use a mesh editor software (Blender, Paraview ..).

About suturing, there is some private plugin simulating suture. More information can be found about it on the marketplace.
Best regards,

Hugo

[SdAuto]

Hi sir,
Thank’s for your answer,
I have a nother question, I tried to compile the file “src/doc/src_exemple/example3” on Qt creator, it showed me an error at the file “scene.h“, and I didn’t found this file in sofa.

Thank’s sir

[Hugo]

Dear SdAuto,

You should rather focus on:

• the online documentation for reading,
• and the examples available in SOFA (in repository examples/)

Best,

Hugo

[SdAuto]

Dear Sir,

I would like to write a scene in cpp but the corresponding help link is still under construction. Could you please give me some guidelines to do it ?

Write a scene in Cpp

Best

[Hugo]

First of all, you can really get inspiration from the Main.cpp from applications/projects/runSofa/.
Here is a short template about how to write a scene in C++:

#include <sstream>
using std::ostringstream ;
#include <fstream>

#include <sofa/helper/ArgumentParser.h>
#include <SofaSimulationCommon/common.h>
#include <sofa/simulation/Node.h>
#include <sofa/helper/system/PluginManager.h>
#include <sofa/simulation/config.h> // #defines SOFA_HAVE_DAG (or not)
#include <SofaSimulationCommon/init.h>
#include <SofaSimulationTree/init.h>
#include <SofaSimulationTree/TreeSimulation.h>

#include <SofaComponentCommon/initComponentCommon.h>
#include <SofaComponentBase/initComponentBase.h>
#include <SofaComponentGeneral/initComponentGeneral.h>
#include <SofaComponentAdvanced/initComponentAdvanced.h>
#include <SofaComponentMisc/initComponentMisc.h>
#include <sofa/helper/BackTrace.h>

// Add any other includes needed by your scene
// #include<path_to/myComponent.h>
// ...

int main(int argc, char** argv)
{
	sofa::helper::BackTrace::autodump();
	ExecParams::defaultInstance()->setAspectID(0);

	// here you can init the GUI you wish
	// as an example, see : applications/projects/runSofa/Main.cpp

    sofa::simulation::tree::init();
	sofa::component::initComponentBase();
    sofa::component::initComponentCommon();
    sofa::component::initComponentGeneral();
    sofa::component::initComponentAdvanced();
    sofa::component::initComponentMisc();

	sofa::simulation::setSimulation(new sofa::simulation::tree::TreeSimulation());

	std::ostringstream no_error_message;
    sofa::helper::system::PluginManager::getInstance().loadPlugin("MyPlugin",&no_error_message);
    sofa::helper::system::PluginManager::getInstance().init();

    // Here start the description of your scene in C++

    // you can create nodes
    sofa::simulation::tree::GNode* groot = new sofa::simulation::tree::GNode;
    groot->setName ("root");
    sofa::defaulttype::Vec3d g = sofa::defaulttype::Vec3d (0,-9.81,0);
    groot->setGravityInWorld(g);

    // you can create components in these nodes
	addMyComponent(groot);

	// you can add new child nodes and repeat the process to build your scene
	sofa::simulation::tree::GNode* childNode = new sofa::simulation::tree::GNode;
 	childNode->setName( "child_of_root" );\r
	groot->addChild(childNode);

	addMyComponent(childNode);

    sofa::simulation::getSimulation()->init(groot.get());
	

    // Run the simulation
    groot->setAnimate(true);

    // close the simulation
    if (groot!=NULL)
        sofa::simulation::getSimulation()->unload(groot);

    sofa::simulation::common::cleanup();
    sofa::simulation::tree::cleanup();
    return 0;
}

// this function illustrates how to add a component to a node
myComponent *addMyComponent(sofa::simulation::tree::GNode *node) {

	myComponent* myComp = new myComponent;
	myComp->setName ("myComponentName");
	myComp->addTag ((Tag)"myTag");
	myComp->d_data.setValue(0.02); // any public data of the component can thus be defined
	node->addObject (myComp);
	
	return (myComponent *)solver;
}

Please let me know if it helps.
If yes, I will add it to the documentation.

Best,

Hugo

[max]

Hi all,

Just to mention that it is *way* easier to write scenes in Python, unless you *really* have to do it in c++.

In any case, the learning curve for grasping SOFA concepts will be much less steep using Python, since you’ll just focus on the scene creation rather than SOFA internal book-keeping.

Should you choose this option, you need to enable the SofaPython plugin during compilation. Then a minimal python scene would look like:

def createScene(node):
    # create a node in the scene graph (i.e. 'Node' in xml scenes)
    child_node = node.createChild('child name') 

    # create a component under the graph node
    child_dofs = child_node.createObject('MechanicalObject', template = 'Vec3', name = 'dofs')

Please refer to the documentation for more.

Hope this helps,

[Hugo]

Yes, thank you max !
I wanted to mention Python and forgot about it !
SdAuto, indeed consider Python which is much more flexible and powerful than C++ only. You could even combine a scene in C++ including a SofaPythonController and use Python scripts as well.

Cheers,

Hugo

[SdAuto]

Dear Sir,
I tried to compile Main.cpp but I found a problem in CMakeLists.txt which seems to me that it is not complete. I mean there are some libraries that are not specified with target_link_librarie. I did not want to add all of them by hand since, I think this will take time to have them all and in the correct order. Could you please help me on this ?
I show you the error I get:
Undefined symbols for architecture x86_64:

“sofa::simulation::getSimulation()”, referenced from:

_main in Main.cpp.o

“sofa::simulation::setSimulation(sofa::simulation::Simulation*)”, referenced from:

_main in Main.cpp.o

“sofa::simulation::tree::TreeSimulation::TreeSimulation()”, referenced from:

_main in Main.cpp.o

“sofa::simulation::tree::init()”, referenced from:

_main in Main.cpp.o

“sofa::simulation::tree::cleanup()”, referenced from:

_main in Main.cpp.o

“sofa::simulation::common::cleanup()”, referenced from:

_main in Main.cpp.o

“sofa::simulation::Visitor::Visitor(sofa::core::ExecParams const*)”, referenced from:

sofa::component::misc::ReadStateActivator::ReadStateActivator(sofa::core::ExecParams const*, bool) in Main.cpp.o

“sofa::simulation::Visitor::~Visitor()”, referenced from:

sofa::component::misc::ReadStateActivator::~ReadStateActivator() in Main.cpp.o

sofa::component::misc::CompareStateCreator::~CompareStateCreator() in Main.cpp.o

“sofa::gui::GUIManager::AddGUIOption(char const*)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::SetDimension(int, int)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::ListSupportedGUI(char)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::CurrentSimulation()”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::Init(char const*, char const*)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::MainLoop(boost::intrusive_ptr<sofa::simulation::Node>, char const*)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::SetScene(boost::intrusive_ptr<sofa::simulation::Node>, char const*, bool)”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::closeGUI()”, referenced from:

_main in Main.cpp.o

“sofa::gui::GUIManager::createGUI(boost::intrusive_ptr<sofa::simulation::Node>, char const*)”, referenced from:

_main in Main.cpp.o

Best,

[SdAuto]

Hi sir,
finally, i have added in CMakeLists the missing libraries and it is working correctly

cmake_minimum_required(VERSION 2.8.12)
project(runSofa)
#modifier..........................................................................
set(SofaFramework_DIR /home/user/sofa/v16.08/build/install/lib/cmake/SofaFramework)
set(TinyXML_DIR /home/user/sofa/v16.08/build/install/lib/cmake/TinyXML)
set(GTest_DIR /home/user/sofa/v16.08/build/install/lib/cmake/GTest)
set(SofaGeneral_DIR/home/user/sofa/v16.08/build/install/lib/cmake)

#..................................................................................
option(RUNSOFA_INSTALL_AS_BUNDLE "Create a bundle containing all the installation files (Only Mac OS X for now)" OFF)
link_directories(/home/user/sofa/v16.08/build/install/lib)
link_directories(/home/user/sofa/v16.08/build/install/lib/cmake/SofaGeneral)
link_directories(/home/user/sofa/v16.08/build/lib)
#.....................................................................................

if(APPLE)
    set(RC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/runSOFA.icns")
else()
    set(RC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/sofa.rc")
endif()

find_package(SofaFramework REQUIRED) # to get SOFA_HAVE_GLUT

if(APPLE)
	set_source_files_properties(${RC_FILES} PROPERTIES MACOSX_PACKAGE_LOCATION "Resources")
endif()

if(APPLE AND RUNSOFA_INSTALL_AS_BUNDLE)
	add_executable(${PROJECT_NAME} MACOSX_BUNDLE ${RC_FILES} Main.cpp )
else()
	add_executable(${PROJECT_NAME} ${RC_FILES} Main.cpp)
endif()

if(APPLE)
	set_target_properties( ${PROJECT_NAME} PROPERTIES MACOSX_BUNDLE_ICON_FILE "runSOFA.icns" )
endif()
#modifier.............................................................
include_directories("/home/user/sofa/v16.08/build/install/include")
include_directories("/home/user/sofa/v16.08/src/applications")
include_directories("/home/user/sofa/v16.08/build/install/lib/cmake")
target_link_libraries(${PROJECT_NAME} SofaComponentGeneral SofaBaseTopology)
#......
target_link_libraries(${PROJECT_NAME} SofaComponentAdvanced SofaComponentMisc)
target_link_libraries(${PROJECT_NAME} SofaSimulationGraph)
target_link_libraries(${PROJECT_NAME} SofaGuiMain)
#.......
target_link_libraries(${PROJECT_NAME} SofaValidation)
target_link_libraries(${PROJECT_NAME} SofaGeneralLoader)
target_link_libraries(${PROJECT_NAME} SofaSimulationCommon)
target_link_libraries(${PROJECT_NAME} SofaSimulationCore)
target_link_libraries(${PROJECT_NAME} SofaSimulationTree)
target_link_libraries(${PROJECT_NAME} SofaCore)
target_link_libraries(${PROJECT_NAME} SofaGuiCommon)
target_link_libraries(${PROJECT_NAME} SofaComponentBase)
target_link_libraries(${PROJECT_NAME} SofaComponentCommon)
#...........................................................................
if(SOFA_HAVE_GLUT)
	target_compile_definitions(${PROJECT_NAME} PUBLIC "SOFA_HAVE_GLUT_GUI")
endif()

if(APPLE AND RUNSOFA_INSTALL_AS_BUNDLE)
	# set(CPACK_COMPONENTS_ALL BundlePack)
	set_property(GLOBAL PROPERTY RUNSOFA_CPACK_COMPONENTS_ALL BundlePack)
	include(cmake/bundle.cmake)
else()
	sofa_install_targets(SofaGui runSofa "")
endif()

thank’s

[Hugo]

Thank you for your feedback.
Here is the documentation page updated.

Do not hesitate to contribute to it.

Best,

Hugo

[Author]

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