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sofagym's Issues

env.reset() error

Hi
I've tried to load a sample in test_env.py, but found an error raising when executed to env.reset().

D:\SofaGym-main>python test_env.py

---------------------------------------
Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: D:\sofa
Using environment variable SOFAPYTHON3_ROOT: D:\sofa\plugins\SofaPython3
---------------------------------------

[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Geometry.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Detection.Algorithm.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Detection.Intersection.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Response.Mapper.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Response.Contact.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Visual.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Setting.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Iterative.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mass.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mapping.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.StateContainer.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Constant.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Grid.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Dynamic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.Spring.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Select.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.ODESolver.Forward.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.ODESolver.Backward.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.IO.Mesh.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Diffusion.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.Elastic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Projective.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.MechanicalLoad.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mapping.MappedMatrix.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Model.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Correction.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Solver.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.AnimationLoop.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.TensorMass.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Analyze.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Generate.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Transform.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Engine.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Direct.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Playback.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SceneUtility.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GUI.Component.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Mapping.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Controller.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.NonUniform.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.HyperElastic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Utility.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Haptics.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Rendering2D.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Rendering3D.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Shader.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Preconditioner.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/SofaComponentAll.dll
Start env  concentrictuberobot-v0
50851
D:\python\lib\site-packages\gym\spaces\box.py:127: UserWarning: WARN: Box bound precision lowered by casting to float32
  logger.warn(f"Box bound precision lowered by casting to {self.dtype}")
D:\python\lib\site-packages\gym\utils\passive_env_checker.py:174: UserWarning: WARN: Future gym versions will require that `Env.reset` can be passed a `seed` instead of using `Env.seed` for resetting the environment random number generator.
  logger.warn(
D:\python\lib\site-packages\gym\utils\passive_env_checker.py:187: UserWarning: WARN: Future gym versions will require that `Env.reset` can be passed `options` to allow the environment initialisation to be passed additional information.
  logger.warn(
All clients are closed. Bye Bye.
{'scene': 'CTR', 'deterministic': True, 'source': [-150, 0, 30], 'target': [0, 0, 30], 'mesh': 'mesh/nasal_cavity.obj', 'scale': 30, 'rotation': [140.0, 0.0, 0.0], 'translation': [0.0, 0.0, 0.0], 'goalList': [[0.0, 0.0, 0.0]], 'goalPos': [0.0, 16.861897843737978, 44.72900560493795], 'scale_factor': 10, 'timer_limit': 50, 'timeout': 3, 'display_size': (1600, 800), 'render': 1, 'save_data': True, 'save_path': 'D:\\SofaGym-main\\sofagym\\envs\\CTR/Results/CTR', 'planning': True, 'discrete': True, 'seed': 0, 'start_from_history': None, 'python_version': 'python3.8', 'zFar': 5000, 'save_path_image': None, 'save_path_results': 'D:\\SofaGym-main\\sofagym\\envs\\CTR/Results/CTR/data', 'dt': 0.01, 'goal_node': 0}
---------------------------------------
Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: D:\sofa
Using environment variable SOFAPYTHON3_ROOT: D:\sofa\plugins\SofaPython3
---------------------------------------
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Geometry.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Detection.Algorithm.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Detection.Intersection.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Response.Mapper.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Collision.Response.Contact.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Visual.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Setting.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Iterative.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mass.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mapping.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.StateContainer.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Constant.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Grid.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Container.Dynamic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.Spring.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Select.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.ODESolver.Forward.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.ODESolver.Backward.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.IO.Mesh.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Diffusion.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.Elastic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Projective.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.MechanicalLoad.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Mapping.MappedMatrix.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Model.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Correction.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Constraint.Lagrangian.Solver.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.AnimationLoop.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.TensorMass.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Analyze.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Generate.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Engine.Transform.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Engine.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Direct.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Playback.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SceneUtility.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GUI.Component.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Mapping.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Controller.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.NonUniform.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.SolidMechanics.FEM.HyperElastic.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Topology.Utility.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.Haptics.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Rendering2D.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Rendering3D.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.GL.Component.Shader.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/Sofa.Component.LinearSolver.Preconditioner.dll
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/SofaComponentAll.dll
SCENE  {'scene': 'CTR', 'deterministic': True, 'source': [-150, 0, 30], 'target': [0, 0, 30], 'mesh': 'mesh/nasal_cavity.obj', 'scale': 30, 'rotation': [140.0, 0.0, 0.0], 'translation': [0.0, 0.0, 0.0], 'goalList': [[0.0, 0.0, 0.0]], 'goalPos': [0.0, 16.861897843737978, 44.72900560493795], 'scale_factor': 10, 'timer_limit': 50, 'timeout': 3, 'display_size': (1600, 800), 'render': 1, 'save_data': True, 'save_path': 'D:\\SofaGym-main\\sofagym\\envs\\CTR/Results/CTR', 'planning': True, 'discrete': True, 'seed': 0, 'start_from_history': None, 'python_version': 'python3.8', 'zFar': 5000, 'save_path_image': None, 'save_path_results': 'D:\\SofaGym-main\\sofagym\\envs\\CTR/Results/CTR/data', 'dt': 0.01, 'goal_node': 0}
[INFO]    [PluginManager] Loaded plugin: D:/sofa/bin/BeamAdapter.dll

########## SIG 11 - SIGSEGV: segfault ##########
  sofa::helper::BackTrace::dump
  sofa::helper::BackTrace::sig
  exp2f
  exp2f
  _C_specific_handler
  _chkstk
  RtlRestoreContext
  KiUserExceptionDispatcher
  PyObject_GetAttrString
  sofapython3::PythonEnvironment::getStaticData
  initExternalModule
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  PyCFunction_Call
  PyObject_MakeTpCall
  Py_FatalError
  Py_CheckFunctionResult
  PyEval_EvalFrameDefault
  Py_CheckFunctionResult
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  Py_CheckFunctionResult
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  Py_CheckFunctionResult
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  PyEval_EvalCodeEx
  PyEval_EvalCode
  PyArena_New
  PyArena_New
  PyRun_FileExFlags
  PyRun_SimpleFileExFlags
  PyRun_AnyFileExFlags
  Py_FatalError
  Py_RunMain
  Py_RunMain
  Py_Main
  Py_Main
  BaseThreadInitThunk
  RtlUserThreadStart
Exception in thread Thread-3:
Traceback (most recent call last):
  File "D:\python\lib\threading.py", line 932, in _bootstrap_inner
    self.run()
  File "D:\python\lib\threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "D:\SofaGym-main\sofagym\rpc_server.py", line 529, in deferredStart
    subprocess.run([sys.executable, path+"sofagym/rpc_client.py", sdict, str(nb_actions), str(port_rpc)],
  File "D:\python\lib\subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['D:\\python\\python.exe', 'D:\\SofaGym-main/sofagym/rpc_client.py', "{'scene': 'CTR', 'deterministic': True, 'source': [-150, 0, 30], 'target': [0, 0, 30], 'mesh': 'mesh/nasal_cavity.obj', 'scale': 30, 'rotation': [140.0, 0.0, 0.0], 'translation': [0.0, 0.0, 0.0], 'goalList': [[0.0, 0.0, 0.0]], 'goalPos': [0.0, 16.861897843737978, 44.72900560493795], 'scale_factor': 10, 'timer_limit': 50, 'timeout': 3, 'display_size': (1600, 800), 'render': 1, 'save_data': True, 'save_path': 'D:\\\\SofaGym-main\\\\sofagym\\\\envs\\\\CTR/Results/CTR', 'planning': True, 'discrete': True, 'seed': 0, 'start_from_history': None, 'python_version': 'python3.8', 'zFar': 5000, 'save_path_image': None, 'save_path_results': 'D:\\\\SofaGym-main\\\\sofagym\\\\envs\\\\CTR/Results/CTR/data', 'dt': 0.01, 'goal_node': 0}", '12', '50851']' returned non-zero exit status 3.

Is there any method to generate image state?

Hi, thank you for great works for SofaGym!

I currently study SofaGym and make my own environment.
In my reinforcement learning architecture, I want to define image state(or observation) which is related to GUI screen image.

For this, I defined additional camera in Scene python file as follows:
(I thought that InteractiveCamera can realize my wish :))

source = config["source"]
target = config["target"]
rootNode.addObject("InteractiveCamera", name='camera2', position=source, lookAt=target, zFar=500)

Next, I refer to viewer.py and find the code which can make image object as follows:

glViewport(0, 0, self.surface_size[0], self.surface_size[1])

glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
glEnable(GL_LIGHTING)
glEnable(GL_DEPTH_TEST)

if self.root:
    Sofa.SofaGL.glewInit()
    Sofa.Simulation.initVisual(self.root)
    glMatrixMode(GL_PROJECTION)
    glLoadIdentity()
    gluPerspective(45, (self.surface_size[0] / self.surface_size[1]), 0.1, self.zFar)

    glMatrixMode(GL_MODELVIEW)
    glLoadIdentity()

    cameraMVM = self.root.camera.getOpenGLModelViewMatrix()

    glMultMatrixd(cameraMVM)
    Sofa.SofaGL.draw(self.root)
else:
    print("===============> ERROR")

try:
    x, y, width, height = glGetIntegerv(GL_VIEWPORT)
except:
    width, height = self.surface_size[0], self.surface_size[1]
buff = glReadPixels(0, 0, width, height, GL_RGB, GL_UNSIGNED_BYTE)

image_array = np.fromstring(buff, np.uint8)
if image_array.shape != (0,):
    image = image_array.reshape(self.surface_size[1], self.surface_size[0], 3)
else:
    image = np.zeros((self.surface_size[1], self.surface_size[0], 3))

image = np.flipud(image)
image = np.moveaxis(image, 0, 1)

I checked that above image is same as GUI screen image.
By using above code and Interactive camera(defined as camera2), I implemented additional function that returns image in Toolbox python file.
However, there is some multi-thread error(I guess that problem is due to reinitialization such as Sofa.SofaGL.glewInit() and Sofa.SofaGL.draw(self.root)).
So I conclude that this is not good approach.

Is there any method to get screen image in Toolbox and Scene code python without GUI?

GL Error

After a clean installation following the README, I run python test_env.py and got the following error regarding the GLSLShader and the viewport:

>>  Init cartstem_config...
>>  Init CartStem...
>>  Init cartstem...
>>  Init done.
>>   Time before start: 0 steps. Initialization ...
>>   ... Done.
Start ...

--------------------------------
EPISODE -  0
--------------------------------

/home/obarbany/miniconda3/envs/ddm/lib/python3.7/site-packages/gym/utils/passive_env_checker.py:220: DeprecationWarning: WARN: Core environment is written in old step API which returns one bool instead of two. It is recommended to rewrite the environment with new step API. 
  "Core environment is written in old step API which returns one bool instead of two. "
/home/obarbany/miniconda3/envs/ddm/lib/python3.7/site-packages/gym/utils/passive_env_checker.py:142: UserWarning: WARN: The obs returned by the `step()` method was expecting numpy array dtype to be float32, actual type: float64
  f"{pre} was expecting numpy array dtype to be {observation_space.dtype}, actual type: {obs.dtype}"
/home/obarbany/miniconda3/envs/ddm/lib/python3.7/site-packages/gym/utils/passive_env_checker.py:165: UserWarning: WARN: The obs returned by the `step()` method is not within the observation space.
  logger.warn(f"{pre} is not within the observation space.")
[INFO]   >>> Time: 0.033739328384399414
[INFO]   >>> RTF: 2.96390013638323
[ERROR]   [GLSLShader] ERROR: Link of program shader failed:
[ERROR]   [GLSLShader] Vertex info
-----------
(0) : error C5145: must write to gl_Position

[ERROR]   [GLSLShader] Fragment shader file: shaders/softShadows/VSM/generate_depth_texture.frag
[ERROR]   [GLSLShader] Vertex shader file: shaders/softShadows/VSM/generate_depth_texture.vert
[ERROR]   [GLSLShader] ERROR: Link of program shader failed:
[ERROR]   [GLSLShader] Vertex info
-----------
(0) : error C5145: must write to gl_Position

[ERROR]   [GLSLShader] Fragment shader file: shaders/softShadows/VSM/blur_texture.frag
[ERROR]   [GLSLShader] Vertex shader file: shaders/softShadows/VSM/blur_texture.vert
[ERROR]   [GLSLShader] ERROR: Link of program shader failed:
[ERROR]   [GLSLShader] Vertex info
-----------
(0) : error C5145: must write to gl_Position

[ERROR]   [GLSLShader] Fragment shader file: shaders/softShadows/VSM/generate_depth_texture.frag
[ERROR]   [GLSLShader] Vertex shader file: shaders/softShadows/VSM/generate_depth_texture.vert
[ERROR]   [GLSLShader] ERROR: Link of program shader failed:
[ERROR]   [GLSLShader] Vertex info
-----------
(0) : error C5145: must write to gl_Position

[ERROR]   [GLSLShader] Fragment shader file: shaders/softShadows/VSM/blur_texture.frag
[ERROR]   [GLSLShader] Vertex shader file: shaders/softShadows/VSM/blur_texture.vert
Step  1  action :  1  reward :  1.0  done: False
[INFO]   >>> Time: 0.03290152549743652
[INFO]   >>> RTF: 3.039372749077892
[ERROR]   [SofaRuntime] GLError: GLError(
	err = 1281,
	description = b'invalid value',
	baseOperation = glViewport,
	cArguments = (0, 0, 1600, 800)
)

On a side note, it looks like the signature of Animationin splib3.animation.animete changed and now requires a realTimeClock boolean as argument.

[Gripper Env] the postion and orientation of gripper won't change

Actually, I don't get familiar with the structure of the sofagym, And I try my best to describe my issue.
I think the executeAnimation is the function of operating the gripper, and setPos is to update the position which is gotten from the getPos function to update the value of the position.

I print the value in the executeAnimation.

Why this function is actuated 5 times in one step?
And Why each actuated previous position is initialized? (Not save the previous value)

image
`

def executeAnimation(fingers, factor):

    # print("In ExecuteAnimation")
    # self.dofs.append(self.node.getChild('PneumaticGripper').getChild('PneumaticFinger'+str(i+1)).mecaObj)
    results0 = moveRestPos(fingers[0].mecaObj.position.value, -1.0, -1.0, -1.0)
    results1 = moveRestPos(fingers[1].mecaObj.position.value, -1.0, -1.0, -1.0)
    print("============")
    print(fingers[0].mecaObj.position.value[0])
    print(results0[0])
    fingers[0].mecaObj.position.value = results0
    print(fingers[0].mecaObj.position.value[0])
    fingers[1].mecaObj.position.value = results1

`
The code may a little different from the Gripper to which I referred.
Moreover, when I run the gripper env, the gripper also not changed position and orientation.

rpc_server issue OSError: [Errno 98] Address already in use

When running simple examples the environments of sofagym, this error happens:

Exception in thread Thread-2 (dispatch):
Traceback (most recent call last):
  File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/usr/lib/python3.10/threading.py", line 953, in run
    self._target(*self._args, **self._kwargs)
  File "/home/samuelyoussef/Documents/SOFA/Plugins/SofaGym/sofagym/rpc_server.py", line 417, in dispatch
    with SimpleThreadedXMLRPCServer(('localhost', port_rpc), requestHandler=RequestHandler) as server:
  File "/usr/lib/python3.10/xmlrpc/server.py", line 605, in __init__
    socketserver.TCPServer.__init__(self, addr, requestHandler, bind_and_activate)
  File "/usr/lib/python3.10/socketserver.py", line 452, in __init__
    self.server_bind()
  File "/usr/lib/python3.10/socketserver.py", line 466, in server_bind
    self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use

Catheter action for RL

Hi, I am trying to use sofa-gym in order to train an agent to move a catheter from one area of a model heart to another. Previously I have been using imitation learning techniques which have been relatively successful. My scene is based on this scene in the beam adapter example. This uses 'InterventionalRadiologyController' to move the catheter. Now I am following the CartPole example and am unsure how to implement the class 'ApplyAction' for my purposes, in order to move the catheter. Any help would be appreciated. Thanks, Mark.

Error on linearSolver

With Sofa v22.12, I got on almost all envs an error :
[ERROR] [LinearSolverConstraintCorrection(GCS)] Can not use the solver linearSolver because it is templated on GraphScatteredType

Some idea ?

I got some warnings too :

[WARNING]` [ShewchukPCGLinearSolver(linearSolver)] String data "preconditioners" is now replaced by explicit data link: "preconditioner" (PR #3155)
[SUGGESTION] [SparseLDLSolver(precond)] Template is empty
By default SparseLDLSolver uses blocks with a single scalar (to handle all cases of simulations).
If you are using only 3D DOFs, you may consider using blocks of Matrix3 to speedup the calculations.
If it is the case, add template="CompressedRowSparseMatrixMat3x3d" to this object in your scene
Otherwise, if you want to disable this message, add template="CompressedRowSparseMatrixd" .
[WARNING] [LinearSolverConstraintCorrection(GCS)] String data "solverName" is now replaced by explicit data link: "linearSolver" (PR #3152)
[WARNING] [ShewchukPCGLinearSolver(linearSolver)] String data "preconditioners" is now replaced by explicit data link: "preconditioner" (PR #3155)
[SUGGESTION] [SparseLDLSolver(precond)] Template is empty
By default SparseLDLSolver uses blocks with a single scalar (to handle all cases of simulations).
If you are using only 3D DOFs, you may consider using blocks of Matrix3 to speedup the calculations.
If it is the case, add template="CompressedRowSparseMatrixMat3x3d" to this object in your scene
Otherwise, if you want to disable this message, add template="CompressedRowSparseMatrixd" .
[WARNING] [LinearSolverConstraintCorrection(GCS)] String data "solverName" is now replaced by explicit data link: "linearSolver" (PR #3152)
[SUGGESTION] [SparseLDLSolver(solver)] Template is empty
By default SparseLDLSolver uses blocks with a single scalar (to handle all cases of simulations).
If you are using only 3D DOFs, you may consider using blocks of Matrix3 to speedup the calculations.
If it is the case, add template="CompressedRowSparseMatrixMat3x3d" to this object in your scene
Otherwise, if you want to disable this message, add template="CompressedRowSparseMatrixd" .
[WARNING] [GenericConstraintCorrection(unnamed)] String data "solverName" is now replaced by explicit data link: "linearSolver" (PR #3152)

For the rest there does not seem to be any others breaks.

Error during GripperScene initialisation

The GripperEnv work but during the scene initialisation (on sofa), i got an error :

[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [1, 336] in triangle 0 [0 1 336] in the provided edge list (@/Gripper/Finger1/container.edges). It shows an inconsistency between the edge list (@/Gripper/Finger1/container.edges) and the triangle list (@/Gripper/Finger1/container.triangles). Either fix the topology (probably in a mesh file), or provide only the triangle list to '/Gripper/Finger1/container' and not the edges. In the latter case, the edge list will be computed from triangles.

The error takes root from here.

SofaGym/sofagym/envs/Gripper/Finger.py

Lines 30 to 32 in 66af7d8

model.addObject('MeshVTKLoader', name='loader', filename=VolumetricMeshPath, scale3d=[1, 1, 1],
translation=translation, rotation=rotation)
model.addObject('TetrahedronSetTopologyContainer', src='@loader', name='container')

I don't know if it comes from the vtkloader or from the mesh itself

Tests and examples

Using the binary, and following the acceptation of the paper, clean the tests and examples to showcase the results in the article

problem with sofagym

Hello all

I'm trying to run sofagym but I'm getting this error as in #12

[ERROR] [SofaRuntime] AttributeError: Missing attribute: addNewData Traceback (most recent call last): File "e:\sofa\sofagym\sofagym/sofagym/rpc_client.py", line 174, in <module> root = init_simulation(config, _startCmd, mode='simu') File "e:\sofa\sofagym\sofagym\sofagym\simulate.py", line 49, in init_simulation create_scene(root, config, mode = mode) File "e:\sofa\sofagym\sofagym\sofagym\envs\Trunk\TrunkScene.py", line 214, in createScene trunk = Trunk(simulation, inverseMode=False) File "E:\SOFA\SOFA_v22.06.00_Win64\plugins\STLIB\lib\python3\site-packages\splib3\objectmodel\__init__.py", line 49, in __call__ o.node.addNewData("Prefab type", "Infos", "","string", str(o.__class__.__name__))

When I change the addNewData to addData inside the splib3 I got this error

[ERROR] [SofaRuntime] TypeError: Invalid Type string: available types are [Edge, Hexa, Link, Mat2x2d, Mat2x2f, Mat3x3d, Mat3x3f, Mat3x4d, Mat3x4f, Mat4x4d, Mat4x4f, Penta, PrefabLink, Quad, Rigid3::VecCoord, Rigid3d::VecCoord, Rigid3f::VecCoord, Tetra, Triangle, Vec2d, Vec2f, Vec3d, Vec3f, Vec4d, Vec4f, Vec6d, Vec6f, bool, double, float, int, string, vector<Edge>, vector<Hexa>, vector<Mat2x2d>, vector<Mat2x2f>, vector<Mat3x3d>, vector<Mat3x3f>, vector<Mat3x4d>, vector<Mat3x4f>, vector<Mat4x4d>, vector<Mat4x4f>, vector<Penta>, vector<Quad>, vector<Tetra>, vector<Triangle>, vector<Vec2d>, vector<Vec2f>, vector<Vec3d>, vector<Vec3f>, vector<Vec4d>, vector<Vec4f>, vector<Vec6d>, vector<Vec6f>, vector<bool>, vector<double>, vector<float>, vector<int>, vector<string>] Traceback (most recent call last): File "e:\sofa\sofagym\sofagym/sofagym/rpc_client.py", line 174, in <module> root = init_simulation(config, _startCmd, mode='simu') File "e:\sofa\sofagym\sofagym\sofagym\simulate.py", line 49, in init_simulation create_scene(root, config, mode = mode) File "e:\sofa\sofagym\sofagym\sofagym\envs\Trunk\TrunkScene.py", line 214, in createScene trunk = Trunk(simulation, inverseMode=False) File "E:\SOFA\SOFA_v22.06.00_Win64\plugins\STLIB\lib\python3\site-packages\splib3\objectmodel\__init__.py", line 49, in __call__ o.node.addData("Prefab type", "Infos", "","string", str(o.__class__.__name__))

Can any one tell how to solve this issue please?

I'm runnign Sofa 22.06 on windows 10

AttributeError: 'numpy.random._generator.Generator' object has no attribute 'seed'

Hello,

python test_env.py -e trunk-v0 -ep 100 -s 100

works fine but when I try:

python rl.py -e trunk-v0 -a PPO

I get the following error:

Traceback (most recent call last):
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/rl.py", line 112, in
agent = Agent(env_name, algo_name, seed, results_dir, max_episode_steps, n_envs)
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/agents/SB3Agent.py", line 18, in init
super().init(env_id, seed, output_dir, max_episode_steps, n_envs)
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/agents/SofaBaseAgent.py", line 79, in init
super().init(env_id, seed, output_dir, max_episode_steps)
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/agents/SofaTestAgent.py", line 82, in init
self.test_env = self.env_make()
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/agents/SofaTestAgent.py", line 154, in env_make
self.env_seed(env)
File "/home/emanuele/Desktop/github/sim/sofa/SofaGym/agents/SofaTestAgent.py", line 170, in env_seed
env.action_space.np_random.seed(self.seed)

OS: Ubuntu 22.04.3 LTS
Sofa: v22.12
SofaGym: just cloned from main branch, and followed the installation instructions

Can you help me please?

Unknown error running SOFAgym TrunkEnv

Hi

I'm trying to compile the example TrunkEnv, using a simple python function:

import gym
import sofagym.envs
import time

import sofagym

env = gym.make('trunk-v0')
observation, info = env.reset()

done = False
while not done:
    action = env.action_space.sample()  # this is where you would insert your policy
    observation, reward, done, info = env.step(action)
    env.render()

    done = terminated or truncated
   
env.close()

The terminal output errors are below. The line "observation, info = env.reset()" seems to be causing this. I'm using the SOFA binaries on Windows 10 with Python 3.7.

[INFO]    [PluginManager] Loaded plugin: C:/Users/Tom/Documents/sofa_build/sofa_build/bin/Sofa.GL.Component.Shader.dll
[INFO]    [PluginManager] Loaded plugin: C:/Users/Tom/Documents/sofa_build/sofa_build/bin/Sofa.Component.LinearSolver.Preconditioner.dll
[INFO]    [PluginManager] Loaded plugin: C:/Users/Tom/Documents/sofa_build/sofa_build/bin/SofaComponentAll.dll
[INFO]    [PluginManager] Loaded plugin: C:/Users/Tom/Documents/sofa_build/sofa_build/bin/STLIB.dll
[INFO]    [PluginManager] Loaded plugin: C:/Users/Tom/Documents/sofa_build/sofa_build/bin/SoftRobots.dll

########## SIG 11 - SIGSEGV: segfault ##########
  sofa::helper::BackTrace::dump
  sofa::helper::BackTrace::sig
  seh_filter_exe
  seh_filter_exe
  _C_specific_handler
  _chkstk
  RtlRaiseException
  KiUserExceptionDispatcher
  PyObject_GetAttrString
  sofapython3::PythonEnvironment::getStaticData
  initExternalModule
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  sofapython3::PythonEnvironment::getPythonCallingPointAsFileInfo
  PyMethodDef_RawFastCallKeywords
  PyCFunction_FastCallKeywords
  PyMethodDef_RawFastCallKeywords
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  PyMethodDef_RawFastCallKeywords
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  PyMethodDef_RawFastCallKeywords
  PyEval_EvalFrameDefault
  PyEval_EvalCodeWithName
  PyEval_EvalCodeEx
  PyEval_EvalCode
  PyArena_Free
  PyRun_FileExFlags
  PyRun_SimpleFileExFlags
  PyRun_AnyFileExFlags
  Py_UnixMain
  Py_UnixMain
  PyErr_NoMemory
  Py_Main
  Py_Main
  Py_Main
  BaseThreadInitThunk
  RtlUserThreadStart
Exception in thread Thread-2:
Traceback (most recent call last):
  File "C:\Program Files\Python37\lib\threading.py", line 926, in _bootstrap_inner
    self.run()
  File "C:\Program Files\Python37\lib\threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "c:\users\tom\documents\sofagym-main\sofagym\rpc_server.py", line 528, in deferredStart
    check=True)
  File "C:\Program Files\Python37\lib\subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['C:\\Program Files\\Python37\\python.exe', 'c:\\users\\tom\\documents\\sofagym-main/sofagym/rpc_client.py', "{'scene': 'Trunk', 'deterministic': True, 'source': [300, 0, 80], 'target': [0, 0, 80], 'goalList': [[40, 40, 100], [-10, 20, 80]], 'start_node': None, 'scale_factor': 5, 'timer_limit': 250, 'timeout': 50, 'display_size': (1600, 800), 'render': 1, 'save_data': False, 'save_image': False, 'save_path': 'c:\\\\users\\\\tom\\\\documents\\\\sofagym-main\\\\sofagym\\\\envs\\\\Trunk/Results/Trunk', 'planning': False, 'discrete': True, 'seed': None, 'start_from_history': None, 'python_version': 'python3', 'dt': 0.01, 'save_path_image': None, 'save_path_results': None, 'goal_node': 1, 'goalPos': [-10, 20, 80]}", '16', '62505']' returned non-zero exit status 3.

[envs] Maze, sofa prefab error

Maze env outputs an error :

[ERROR]   [SofaRuntime] AttributeError: Unable to find attribute: addNewData
Traceback (most recent call last):
  File "/home/hunoutl/SOFA/SofaGym/sofagym/rpc_client.py", line 174, in <module>
    root = init_simulation(config, _startCmd, mode='simu')
  File "/home/hunoutl/SOFA/SofaGym/sofagym/simulate.py", line 49, in init_simulation
    create_scene(root,  config, mode = mode)
  File "/home/hunoutl/SOFA/SofaGym/sofagym/envs/Maze/MazeScene.py", line 201, in createScene
    tripod = Tripod(scene.Modelling)
  File "/home/hunoutl/SOFA/sofa/build/sofa_gym_v2212/lib/python3/site-packages/splib3/objectmodel/__init__.py", line 47, in __call__
    o = self.cls(*args, **kwargs)
  File "/home/hunoutl/SOFA/SofaGym/sofagym/envs/Maze/MazeScene.py", line 63, in __init__
    arm = ActuatedArm(self.node, name=name,
  File "/home/hunoutl/SOFA/sofa/build/sofa_gym_v2212/lib/python3/site-packages/splib3/objectmodel/__init__.py", line 47, in __call__
    o = self.cls(*args, **kwargs)
  File "/home/hunoutl/SOFA/SofaGym/sofagym/envs/Maze/actuatedarm.py", line 70, in __init__
    self.servomotor = ServoMotor(self.node, translation=translation, rotation=eulerRotation, indice=int(name[-1]))
  File "/home/hunoutl/SOFA/sofa/build/sofa_gym_v2212/lib/python3/site-packages/splib3/objectmodel/__init__.py", line 49, in __call__
    o.node.addNewData("Prefab type", "Infos", "","string", str(o.__class__.__name__))

This comes from sofa prefab obviously when applied to class ServoMotor(SofaObject)

Make SOFA Binary

Make SOFA binary and test code with binary

Need to add a SOFA Binary with compiled plugins to allow to test the code and free users from compiling SOFA from scratch
Needed plugins:
SP3
STLIB
SoftRobots
SoftRobots.Inverse
BeamAdapter
Cosserat
MOR

AVEC

Add reference to AVEC code and stop porting it here

Unknown Error

Hi!
I have installed SOFA v22.12 on a virtual machine with Ubuntu 22.04LTS.
I am trying to run the example test script and it throws an error I am not sure how to fix:

(sofa) vboxuser@Sofa:~/Downloads/SofaGym$ python test_env.py -e trunk-v0 -ep 100 -s 100
---------------------------------------
Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: /home/vboxuser/SOFA/v22.12.00
---------------------------------------
pygame 2.5.0 (SDL 2.28.0, Python 3.8.17)
Hello from the pygame community. https://www.pygame.org/contribute.html
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.so
56975
/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/site-packages/gym/spaces/box.py:73: UserWarning: WARN: Box bound precision lowered by casting to float32
  logger.warn(
Start env  trunk-v0
---------------------------------------
Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: /home/vboxuser/SOFA/v22.12.00
---------------------------------------
pygame 2.5.0 (SDL 2.28.0, Python 3.8.17)
Hello from the pygame community. https://www.pygame.org/contribute.html
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/plugins/STLIB/lib/libSTLIB.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/plugins/SoftRobots/lib/libSoftRobots.so
[DEPRECATED] [SofaSparseSolver] SofaSparseSolver is deprecated. It will be removed at v23.06. Use Sofa.Component.LinearSolver.Direct instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.LinearSolver.Direct.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaSparseSolver/lib/libSofaSparseSolver.so
[DEPRECATED] [SofaPreconditioner] SofaPreconditioner is deprecated. It will be removed at v23.06. Use Sofa.Component.LinearSolver.Preconditioner and Sofa.Component.LinearSolver.Iterative instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.LinearSolver.Preconditioner.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.LinearSolver.Iterative.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaPreconditioner/lib/libSofaPreconditioner.so
[INFO]    [SofaPython3] Initializing with python version 3.8.17 (default, Jul  5 2023, 21:04:15) 
[GCC 11.2.0]
[INFO]    [SofaPython3] Shared library name is 'libpython3.8m.so'
[INFO]    [SofaPython3] Added '/home/vboxuser/SOFA/v22.12.00/plugins/SofaPython3/lib/python3/site-packages' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/plugins/SofaPython3/lib/libSofaPython3.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/plugins/BeamAdapter/lib/libBeamAdapter.so
[DEPRECATED] [SofaOpenglVisual] SofaOpenglVisual is deprecated;. Use Sofa.GL.Component.Rendering2D, Sofa.GL.Component.Rendering3D and Sofa.GL.Component.Shader instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.GL.Component.Rendering2D.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.GL.Component.Rendering3D.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.GL.Component.Shader.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaOpenglVisual/lib/libSofaOpenglVisual.so
[DEPRECATED] [SofaMiscCollision] SofaMiscCollision is deprecated. It will be removed at v23.06. Use Sofa.Component.Collision.Geometry, Sofa.Component.Collision.Detection.Intersection and Sofa.Component.Collision.Response.Contact instead.
[DEPRECATED] [SofaMiscCollision] If you are looking for OBB and Capsule-related components, please use the external plugin CollisionOBBCapsule.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Collision.Geometry.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Collision.Detection.Intersection.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Collision.Response.Contact.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaMiscCollision/lib/libSofaMiscCollision.so
[DEPRECATED] [SofaBoundaryCondition] SofaBoundaryCondition is deprecated. It will be removed at v23.06. You may use Sofa.Component.Constraint.Projective and Sofa.Component.MechanicalLoad instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Constraint.Projective.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.MechanicalLoad.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaBoundaryCondition/lib/libSofaBoundaryCondition.so
[DEPRECATED] [SofaConstraint] SofaConstraint is deprecated. It will be removed at v23.06. You may use Sofa.Component.Mapping.MappedMatrix, Sofa.Component.Constraint.Lagrangian.Model, Sofa.Component.Constraint.Lagrangian.Correction, Sofa.Component.Constraint.Lagrangian.Solver, Sofa.Component.AnimationLoop, Sofa.Component.Collision.Detection.Intersection and Sofa.Component.Collision.Response.Contact instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Mapping.MappedMatrix.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Constraint.Lagrangian.Model.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Constraint.Lagrangian.Correction.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Constraint.Lagrangian.Solver.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.AnimationLoop.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaConstraint/lib/libSofaConstraint.so
[DEPRECATED] [SofaEngine] SofaEngine is deprecated. It will be removed at v23.06. Use Sofa.Component.Engine.Select instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Engine.Select.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaEngine/lib/libSofaEngine.so
[DEPRECATED] [SofaImplicitOdeSolver] SofaImplicitOdeSolver is deprecated. It will be removed at v23.06. Use Sofa.Component.ODESolver.Backward instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.ODESolver.Backward.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaImplicitOdeSolver/lib/libSofaImplicitOdeSolver.so
[DEPRECATED] [SofaLoader] SofaLoader is deprecated. It will be removed at v23.06. Use Sofa.Component.IO.Mesh instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.IO.Mesh.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaLoader/lib/libSofaLoader.so
[DEPRECATED] [SofaSimpleFem] SofaSimpleFem is deprecated;. It will be removed at v23.06. You may use Sofa.Component.Diffusion and Sofa.Component.SolidMechanics.FEM.Elastic instead.
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.Diffusion.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/lib/libSofa.Component.SolidMechanics.FEM.Elastic.so
[INFO]    [PluginManager] Loaded plugin: /home/vboxuser/SOFA/v22.12.00/collections/SofaSimpleFem/lib/libSofaSimpleFem.so
[WARNING] [GenericConstraintCorrection(unnamed)] String data "solverName" is now replaced by explicit data link: "linearSolver" (PR #3152)
[DEPRECATED] [BruteForceDetection(BruteForceDetection)] As a replacement, use a BroadPhase component, such as [BruteForceBroadPhase, IncrSAP],  
  AND a NarrowPhase component, such as [BVHNarrowPhase, DirectSAPNarrowPhase, IncrSAP, RayTraceNarrowPhase].  
  BruteForceBroadPhase and BVHNarrowPhase have been automatically added to your scene for backward compatibility.
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast
X Error of failed request:  BadValue (integer parameter out of range for operation)
  Major opcode of failed request:  148 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  106
  Current serial number in output stream:  107
(sofa) vboxuser@Sofa:~/Downloads/SofaGym$ [ERROR]   [SofaRuntime] ConnectionRefusedError: [Errno 111] Connection refused
Traceback (most recent call last):
  File "/home/vboxuser/Downloads/SofaGym/sofagym/rpc_client.py", line 181, in <module>
    task = s.getNextTask(stateId)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1109, in __call__
    return self.__send(self.__name, args)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1450, in __request
    response = self.__transport.request(
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1153, in request
    return self.single_request(host, handler, request_body, verbose)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1165, in single_request
    http_conn = self.send_request(host, handler, request_body, verbose)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1278, in send_request
    self.send_content(connection, request_body)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/xmlrpc/client.py", line 1308, in send_content
    connection.endheaders(request_body)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/http/client.py", line 1251, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/http/client.py", line 1011, in _send_output
    self.send(msg)
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/http/client.py", line 951, in send
    self.connect()
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/http/client.py", line 922, in connect
    self.sock = self._create_connection(
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/socket.py", line 808, in create_connection
    raise err
  File "/home/vboxuser/anaconda3/envs/sofa/lib/python3.8/socket.py", line 796, in create_connection
    sock.connect(sa)

Question about Animation

Hi! I built a environment and noticed that when the step(action) function of my environment is called, it actually executes the action twice. I suspect that the problem is with the following code in the function startCmd_EnvName in the toolbox file:
rootNode.AnimationManager.addAnimation( Animation( onUpdate=executeAnimation, params={"cable": cable, "displacement": displacement}, duration=duration, mode="once"))
I noticed that increasing the value of the variable duration increases the number of times the action gets executed, and that the number of times the action gets executed depends on environments (For instance, in the Trunk environment, its displace function gets called 5 times everytime the function startCmd_Trunk gets called, but in CartPole, the function apply_action gets called 10 times). Could anyone please explain the design idea behind this? Should I setup my environment such that the action is only executed once everytime I call the step function? If so, how? Thank you!

Error: splib3 not found

Hi all, I just installed SofaGym. I tried to run the test_env.py file and got this error:

Traceback (most recent call last):
File "test_env.py", line 23, in
from sofagym.envs import *
File "/home/william/SofaGym/sofagym/envs/init.py", line 1, in
from sofagym.envs.BubbleMotion.BubbleMotionEnv import *
File "/home/william/SofaGym/sofagym/envs/BubbleMotion/BubbleMotionEnv.py", line 11, in
from sofagym.AbstractEnv import AbstractEnv
File "/home/william/SofaGym/sofagym/AbstractEnv.py", line 20, in
import splib3
ModuleNotFoundError: No module named 'splib3'

I have installed all the plugins listed in README. Any idea how I should fix this? Thank you!

ConcentricTubeRobot Example Error

Current configuration:
Ubuntu 20.04
Sofa v23.06.00 (From Binary)
Python 3.8.10

When running example (python test_env.py -e concentrictuberobot-v0 -ep 100 -s 100), simulation runs successfully, but when throws this error when training (python rl.py -e concentrictuberobot-v0 -a DQN)

  [SofaRuntime] UFuncTypeError: ufunc 'subtract' did not contain a loop with signature matching types (dtype('<U1'), dtype('float64')) -> None
Traceback (most recent call last):
  File "rl.py", line 114, in <module>
    agent.fit(total_timesteps)
  File "/home/ubuntu20_sofa/SofaGym/agents/SB3Agent.py", line 309, in fit
    self.model.learn(total_timesteps=total_timesteps, reset_num_timesteps=False,
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/dqn/dqn.py", line 265, in learn
    return super().learn(
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/off_policy_algorithm.py", line 334, in learn
    rollout = self.collect_rollouts(
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/off_policy_algorithm.py", line 567, in collect_rollouts
    new_obs, rewards, dones, infos = env.step(actions)
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/base_vec_env.py", line 163, in step
    return self.step_wait()
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/vec_monitor.py", line 76, in step_wait
    obs, rewards, dones, infos = self.venv.step_wait()
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/vec_normalize.py", line 197, in step_wait
    infos[idx]["terminal_observation"] = self.normalize_obs(infos[idx]["terminal_observation"])
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/vec_normalize.py", line 240, in normalize_obs
    obs_ = self._normalize_obs(obs, self.obs_rms).astype(np.float32)
  File "/home/ubuntu20_sofa/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/vec_normalize.py", line 216, in _normalize_obs
    return np.clip((obs - obs_rms.mean) / np.sqrt(obs_rms.var + self.epsilon), -self.clip_obs, self.clip_obs)

Any advice here? I'm pretty sure that I have installed all of the dependencies correctly according to the readme, and this issue is confirmed on multiple installs/machines.

Rendering issue

There's an issue in the environments' gui when the render argument is activated, the simulation window crashes with this error:

/home/samuelyoussef/.local/lib/python3.10/site-packages/glfw/__init__.py:916: GLFWError: (65544) b'EGL: Failed to make context current: EGL cannot access a requested resource'
  warnings.warn(message, GLFWError)

########## SIG 11 - SIGSEGV: segfault ##########
  sofa::helper::BackTrace::sig(int)
  glfwCreateWindow
  _PyObject_MakeTpCall
  _PyEval_EvalFrameDefault
  _PyFunction_Vectorcall
  _PyEval_EvalFrameDefault
  _PyFunction_Vectorcall
  _PyObject_FastCallDictTstate
  _PyObject_MakeTpCall
  _PyEval_EvalFrameDefault
  _PyEval_EvalFrameDefault
  _PyEval_EvalFrameDefault
  PyEval_EvalCode
  _PyRun_SimpleFileObject
  _PyRun_AnyFileObject
  Py_RunMain
  Py_BytesMain
  __libc_start_main
  _start
Segmentation fault (core dumped)
[ERROR]   [SofaRuntime] ConnectionRefusedError: [Errno 111] Connection refused
Traceback (most recent call last):
  File "/home/samuelyoussef/Documents/SOFA/Plugins/SofaGym/sofagym/rpc_client.py", line 181, in <module>
    task = s.getNextTask(stateId)
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1122, in __call__
    return self.__send(self.__name, args)
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1464, in __request
    response = self.__transport.request(
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1166, in request
    return self.single_request(host, handler, request_body, verbose)
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1178, in single_request
    http_conn = self.send_request(host, handler, request_body, verbose)
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1291, in send_request
    self.send_content(connection, request_body)
  File "/usr/lib/python3.10/xmlrpc/client.py", line 1321, in send_content
    connection.endheaders(request_body)
  File "/usr/lib/python3.10/http/client.py", line 1277, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1037, in _send_output
    self.send(msg)
  File "/usr/lib/python3.10/http/client.py", line 975, in send
    self.connect()
  File "/usr/lib/python3.10/http/client.py", line 941, in connect
    self.sock = self._create_connection(
  File "/usr/lib/python3.10/socket.py", line 845, in create_connection
    raise err
  File "/usr/lib/python3.10/socket.py", line 833, in create_connection
    sock.connect(sa)

I temporarily fixed the issue by moving the glfw create window function before the pygame initialization

SofaGym/sofagym/viewer.py

Lines 101 to 105 in 5f4a017

if not glfw.init():
sys.exit(1)
glfw.window_hint(glfw.VISIBLE, False)
self.window = glfw.create_window(self.surface_size[0], self.surface_size[1], "hidden window", None, None)

now the rendering is working but the simulation window keeps showing a not responding message while running.

Error in clean_registry during long runs

Unsure if this is caused by an issue related to #58, but after a seemingly arbitrary number of steps (~60k) in a slightly modified version of the CatheterBeam example, I see this error:

[WARNING] [LCPConstraintSolver(LCPConstraintSolver)] No convergence in unbuilt nlcp gaussseidel function : error =0.000597259 after 1000 iterations
Process ForkServerProcess-3:
Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/rbasdeo/.local/lib/python3.8/site-packages/stable_baselines3/common/vec_env/subproc_vec_env.py", line 34, in _worker
    observation = env.reset()
  File "/home/rbasdeo/.local/lib/python3.8/site-packages/gym/wrappers/time_limit.py", line 27, in reset
    return self.env.reset(**kwargs)
  File "/home/rbasdeo/.local/lib/python3.8/site-packages/gym/wrappers/order_enforcing.py", line 16, in reset
    return self.env.reset(**kwargs)
  File "/home/rbasdeo/sofaGym/sofaGym_catheter/sofagym/envs/CatheterBeamSingle/CatheterBeamSingleEnv.py", line 75, in reset
    super().reset()
  File "/home/rbasdeo/sofaGym/sofaGym_catheter/sofagym/AbstractEnv.py", line 380, in reset
    self.clean()
  File "/home/rbasdeo/sofaGym/sofaGym_catheter/sofagym/AbstractEnv.py", line 276, in clean
    clean_registry(self.past_actions)
  File "/home/rbasdeo/sofaGym/sofaGym_catheter/sofagym/rpc_server.py", line 539, in clean_registry
    actions_to_stateId.pop(str(instances[id]['history']))
KeyError: 'history'

Stable_baselines params:
DQN:
init_kwargs:
policy: 'MlpPolicy'
learning_rate: 0.0005
buffer_size: 4000
learning_starts: 1000
batch_size: 32
gamma: 1.0
train_freq: (1, 'step')
gradient_steps: 1
replay_buffer_class: null
replay_buffer_kwargs: null
optimize_memory_usage: False
target_update_interval: 500
exploration_fraction: 0.1
exploration_initial_eps: 1.0
exploration_final_eps: 0.02
max_grad_norm: 10
policy_kwargs: "dict(net_arch=[128, 128], optimizer_class=th.optim.Adam)"
device: "auto"
fit_kwargs:
total_timesteps: 3200000
max_episode_steps: 300
eval_freq: 10000
n_eval_episodes: 10
save_freq: 10000
video_length: 500

[ERROR] Connection Refused

I am running a simple code like
import gym import sofagym.envs env = gym.make('trunk-v0') env.reset()
The I get the Error like:
[ERROR] [SofaRuntime] ConnectionRefusedError: [Errno 111] Connection refused

How can I fix it? Thanks.

[envs] SimpleMaze, component removed

SimpleMaze contains components that have been removed from Sofa.
I tried some tweaks on the sphere object but it wasn't great and this is only the 1st mistake of this type. I think this scene has others.
The error output:

[ERROR]   [SofaRuntime] ValueError: Object type Sphere<> was not created  
The object is not in the factory.  
This component has been REMOVED since SOFA v20.06 (deprecated since v19.12). Please consider updating your scene. If this component is crucial to you please report that to sofa-dev@ so that we can reconsider this component for future re-integration.  

Traceback (most recent call last):
  File "/home/hunoutl/SOFA/SofaGym/sofagym/rpc_client.py", line 174, in <module>
    root = init_simulation(config, _startCmd, mode='simu')
  File "/home/hunoutl/SOFA/SofaGym/sofagym/simulate.py", line 49, in init_simulation
    create_scene(root,  config, mode = mode)
  File "/home/hunoutl/SOFA/SofaGym/sofagym/envs/SimpleMaze/SimpleMazeScene.py", line 86, in createScene
    sphere.addObject("Sphere", radius='2.0', name='0', color=[255, 0, 0, 255])

[ERROR]   [SofaRuntime] ValueError: Object type Triangle<> was not created  
The object is not in the factory.  
This component has been REMOVED since SOFA v20.06 (deprecated since v19.12). Please consider updating your scene. If this component is crucial to you please report that to sofa-dev@ so that we can reconsider this component for future re-integration.  

Traceback (most recent call last):
  File "/home/hunoutl/SOFA/SofaGym/sofagym/rpc_client.py", line 174, in <module>
    root = init_simulation(config, _startCmd, mode='simu')
  File "/home/hunoutl/SOFA/SofaGym/sofagym/simulate.py", line 49, in init_simulation
    create_scene(root,  config, mode = mode)
  File "/home/hunoutl/SOFA/SofaGym/sofagym/envs/SimpleMaze/SimpleMazeScene.py", line 118, in createScene
    maze.addObject("Triangle", group=1)

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