A Simulation Framework for Magnetic Continuum Robots

Roland Dreyfus, Quentin Boehler, Bradley J. Nelson

Multimedia materials and source code

Description

The magnetic continuum robot (m-CR) simulator is an object-oriented Python implementation of SOFA to simulate magnetically actuated continuum robots. The package interfaces magnetic field models with the SOFA simulated mechanical model of the continuum robot. SOFA (Simulation Open Framework Architecture) is an open-source framework primarily targeted at real-time simulation, with an emphasis on medical simulation.

Installation

This requires Ubuntu 20.04 with Python 3.

Install and build SOFA

Follow the instructions here to build SOFA with Linux.

This code was tested with v.21.12 for SOFA and the external plugins.

Build SOFA and include the following external plugins using these instructions:

• BeamAdapter
• SoftRobots
• STLIB

Make sure to use the same version for SOFA and the plugins (these instructions were tested with v21.12), and to load these plugins in the plugin manager of runSofa.

In CMake GUI, make sure to configure the path to the external plugins in the CMake variable SOFA_EXTERNAL_DIRECTORIES, and check the following boxes:

• PLUGIN_BEAMADAPTER
• PLUGIN_SOFAIMPLICITFIELD
• PLUGIN_SOFADISTANCEGRID
• PLUGIN_PLUGINEXAMPLE
• PLUGIN_STLIB
• PLUGIN_SOFTROBOTS
• SOFA_FETCH_SOFAPYTHON3 (make sure to follow these guidelines for a proper installation of SofaPython3, and make sure you load SofaPython3 via the plugin manager of runSofa)

Make sure the box for PLUGIN_SOFAPYTHON is unchecked.

Install the dependencies

This repository has the following dependencies:

• mag_manip: toolbox for electromagnetic navigation systems (eMNS) modelling.

For installing mag_manip using pip:

pip install mag-manip

Usage simulator

Run simulation using shell commands and SOFA user interface

• Open a terminal and go to the /bin directory of SOFA

./runSofa

• File/Open to open the scene (extentions *.scn or *.pyscn)
• Press "Animate" to start the scene

More information on how to use SOFA here.

Manual navigation using keyboard commands.

• Insertion/retraction

  • CTRL + up/down: insertion/retraction of the m-CR

• Magnetic field

  • CTRL + I/K: inclination angle
  • CTRL + J/L: azimuth angle

Usage python scripts

An example of how to build an m-CR simulation scene can be found in

• example_aortic_arch.py
• example_flat.py.

Example with step-by-step explanation

Below is a step-by-step explanation of how to build an m-CR simulation scene. The explanation is based on example_aortic_arch.py.

Import the mcr_simulation modules

from mcr_simulation import \
    mcr_environment, mcr_instrument, mcr_emns, mcr_simulator, \
    mcr_controller_sofa, mcr_magnet

Load or define the simulation parameters:

# Calibration file for eMNS
cal_path = '../../calib/Navion_2_Calibration_24-02-2020.yaml'

# Parameters instrument
young_modulus_body = 170e6  # (Pa)
young_modulus_tip = 21e6    # (Pa)
length_body = 0.5           # (m)
length_tip = 0.034          # (m)
outer_diam = 0.00133        # (m)
inner_diam = 0.0008         # (m)

length_init = .35

# Parameters environment
environment_stl = '../../mesh/J2-Naviworks.stl'

# Parameter magnet
magnet_length = 4e-3        # (m)
magnet_id = 0.86e-3         # (m)
magnet_od = 1.33e-3         # (m)
magnet_remanence = 1.45     # (T)

# Parameter for beams
nume_nodes_viz = 600
num_elem_body = 30
num_elem_tip = 3

# Transforms
# Sofa sim frame in eMNS

# Transforms (translation , quat)
T_sim_mns = [
    0., 0., 0.,
    0., 0., 0., 1]

# Environment in sofa sim frame
T_env_sim = [
    0., -0.45, 0.,
    -0.7071068, 0, 0, 0.7071068]

# Starting pose sofa_sim frame
T_start_sim = [
  -.075, -.001, -.020, 0.,
  -0.3826834, 0., 0.9238795]

To build an m-CR simulation, start by creating the SOFA scene:

def createScene(root_node):
    ''' Build SOFA scene '''

Add the simulation physics and solver. The mcr_simulator object defines the solver settings and adds gravity, friction, constraints, etc.

    # simulator
    simulator = mcr_simulator.Simulator(
        root_node=root_node)

Define the electromagnetic navigation system. The mcr_emns class uses mag_manip to model the magnetic field and provides methods to compute currents from magnetic fields (backward model) and magnetic fields from currents (forward model).

    # eMNS
    navion = mcr_emns.EMNS(
        name='Navion',
        calibration_path=cal_path)

Add the environment. The mcr_environment object adds the mechanical, collision and visual models of the envirnoment (e.g. anatomical model or collision objects) to the SOFA scene.

    # environment
    environment = mcr_environment.Environment(
        root_node=root_node,
        environment_stl=environment_stl,
        name='aortic_arch',
        T_env_sim=T_env_sim,
        flip_normals=True,
        color=[1., 0., 0., 0.3])

Define the magnets that are embedded in the m-CR body. A magnet object can be created with the mcr_magnet class.

    # magnet
    magnet = mcr_magnet.Magnet(
           length=magnet_length,
           outer_diam=magnet_od,
           inner_diam=magnet_id,
           remanence=magnet_remanence)

The magnetic elements of the instrument are defined by a list with the same length as the proximal section of the instrument num_elem_tip. The magnets should be stored at the index of the instrument element that is magnetic.

    # magnets on both ends of flexible segment
    magnets = [0. for i in range(num_elem_tip)]
    magnets[0] = magnet
    magnets[-1] = magnet

Create the magnetic instrument object. The mcr_instrument class adds the mechanical, collision, and visual model to the SOFA scene.

    # instrument
    instrument = mcr_instrument.Instrument(
        name='mcr',
        root_node=root_node,
        length_body=length_body,
        length_tip=length_tip,
        outer_diam=outer_diam,
        inner_diam=inner_diam,
        young_modulus_body=young_modulus_body,
        young_modulus_tip=young_modulus_tip,
        magnets=magnets,
        num_elem_body=num_elem_body,
        num_elem_tip=num_elem_tip,
        nume_nodes_viz=nume_nodes_viz,
        T_start_sim=T_start_sim,
        color=[.2, .8, 1., 1.]
        )

Create the controller. The controller interfaces with the SOFA controller and with the magnetic field controller. On keyboard events, the desired magnetic field and insertion inputs are sent to the controllers.

    # sofa-based controller
    controller_sofa = mcr_controller_sofa.ControllerSofa(
        root_node=root_node,
        e_mns=navion,
        instrument=instrument,
        length_init=length_init,
        T_sim_mns=T_sim_mns,
    )
    root_node.addObject(controller_sofa)

Post-processing and figure generation

Launch Jupyter notebook

Data processing and figure generation was done in jupiter notebook.

To launch Jupyter open a terminal, go to the directory ral_22_sofa_magnetic, and launch jupyter notebook. This will open a web browser window.

jupyter notebook notebook/ral_2022_mCR_data_viz.ipynb

Tip tracker

Run two-color tip tracker

To run the tracker open a terminal, go to the directory ral_22_sofa_magnetic, and run the python script:

python3 python/instrument_tracker.py -v video/MVI_9976.mp4

Contact: Roland Dreyfus: dreyfusr@ethz.ch, Quentin Boehler: qboehler@ethz.ch