Tracking marker positions while moving limb with prescribed functions

[Rejin Varghese]

Dear experts,

I am a beginner with OpenSim. I have a scaled upper-limb model with a marker set. I wanted to perform some simulations in which I move a particular joint with some prescribed functions, and wanted to get the paths traversed by the different markers over the entire joint movement. How do I go about doing this? Following the forums I have the following, but am not sure if I am doing it right.

Prescribing movement to the shoulder joint

Code: Select all

% get shoulder elevation and elv angle coordinate
elvAngleCoord.setDefaultValue(0.0);
elvAngleCoord.setDefaultIsPrescribed(1);
shoulderElvCoord.setDefaultValue(initialAngle);
shoulderElvCoord.setDefaultIsPrescribed(1);

% create time & joint angle arrays and add points to spline
for i = 1:numSteps
    % create time and joint angle array elements
    time_temp = (finalTime/numSteps)*i;
    time.append(time_temp);
    jointAngle_temp = ((finalAngle-initialAngle)/numSteps)*i;
    shoulderElvAngle.append(jointAngle_temp);
    % add time and joint angle elements to spline
    spline.addPoint(time.get(i-1),shoulderElvAngle.get(i-1));

end
% prescribe motion for shoulder elevation
shoulderElvCoord.setPrescribedFunction(spline);
shoulderElvCoord.setDefaultIsPrescribed(1);

Get global coordinates of markers

Code: Select all

% get marker set
markerSet = model.getMarkerSet();
numMarkers = markerSet.getSize();

% Initializing the model
states = model.initSystem();

% get global coordinates of markers
for i = 1:numMarkers
    local_markerPos(i) = markerSet.get(i-1).getOffset();
    markerParent(i) = markerSet.get(i-1).getBody();
    markerName(i) = markerSet.get(i-1).getName();
    model.getSimbodyEngine().getPosition(states,markerParent(i),local_markerPos(i),temp);
    global_markerPos.push_back(temp);
end

Could you please guide me on whether I am doing it correct? What would I need to do next to get the global marker coordinates over time? I tried running the forward tool, but even after 1hr it hadn't finished executing even between 0 and 0.1secs.

Any help is appreciated.

With sincere regards,

Rejin

The full code I have right now is as follows:

Code: Select all

% import Opensim classes
import org.opensim.modeling.*
% load model
model = Model(['SSM_Ali_scaled.osim']);

global_markerPos = SimTKArrayVec3();
temp = Vec3();
time = ArrayDouble();
shoulderElvAngle = ArrayDouble();
elvAngle = ArrayDouble();
spline = SimmSpline();


%% Coordinate Set 

coordinateSet = model.getCoordinateSet();
numCoordinates = coordinateSet.getSize();

for i = 1:numCoordinates
   coordinateNames(i) =  coordinateSet.get(i-1).getName();
   if strcmp(coordinateNames(i),'elv_angle')
       elv_angle_index = i;
   end
   if strcmp(coordinateNames(i),'shoulder_elv')
       shoulder_elv_index = i;
   end
end

shoulderElvCoord = coordinateSet.get(shoulder_elv_index-1);
elvAngleCoord = coordinateSet.get(elv_angle_index-1);

%% Movement Set

numSteps = 100;
finalTime = 5;
initialAngle = pi/6;
finalAngle = pi/2;

% get shoulder elevation and elv angle coordinate
elvAngleCoord.setDefaultValue(0.0);
elvAngleCoord.setDefaultIsPrescribed(1);
shoulderElvCoord.setDefaultValue(initialAngle);
shoulderElvCoord.setDefaultIsPrescribed(1);

% create time & joint angle arrays and add points to spline
for i = 1:numSteps
    % create time and joint angle array elements
    time_temp = (finalTime/numSteps)*i;
    time.append(time_temp);
    jointAngle_temp = ((finalAngle-initialAngle)/numSteps)*i;
    shoulderElvAngle.append(jointAngle_temp);
    % add time and joint angle elements to spline
    spline.addPoint(time.get(i-1),shoulderElvAngle.get(i-1));

end
% prescribe motion for shoulder elevation
shoulderElvCoord.setPrescribedFunction(spline);
shoulderElvCoord.setDefaultIsPrescribed(1);

%% Marker Set (local and global coordinates)

% get marker set
markerSet = model.getMarkerSet();
numMarkers = markerSet.getSize();

% Initializing the model
states = model.initSystem();

% get global coordinates of markers
for i = 1:numMarkers
    local_markerPos(i) = markerSet.get(i-1).getOffset();
    markerParent(i) = markerSet.get(i-1).getBody();
    markerName(i) = markerSet.get(i-1).getName();
    model.getSimbodyEngine().getPosition(states,markerParent(i),local_markerPos(i),temp);
    global_markerPos.push_back(temp);
end


%% Create splines based on F,SF,SR & R markers


%% Set up the visualizer to show the model and simulation
model.setUseVisualizer(false);

%% DEFINE SOME PARAMETERS FOR THE SIMULATION

% Define the new tool object which will be run
tool = ForwardTool(); %--> to see all properties which can be set type 'methodsview(tool)'

% Define the model which the forward tool will operate on
tool.setModel(model);

% Define the start and finish times for simulation
tool.setStartTime(0);
tool.setFinalTime(0.1);
tool.setSolveForEquilibrium(true);

% Define the name of the forward analysis
tool.setName('tendonAnalysisModel');

% Run the simulation
tool.run();  %--> rotate the view to see the tug of war simulation