Muscle parameters

[Mohammadreza Rezaie]

Hi,

I have a loop that compute fiber force, length and muscle moment arm. I'm dealing with these issues and wondering if anyone could guide me.

1. computeMomentArm doesn't get joint angles from state and I have to put them in coordinate that makes the code extremely slow. Without coordinate, the outputs are different.

2. The output of getFiberForce and getFiberLength with and without the computeMomentArm in the loop are different.

Here is the code (q2 and u2 are 2D arrays of joint angles and angular velocities)

Code: Select all

for i=1:frame
	Q = Vector(); Q.resize(nCoordinates);
	U = Vector(); U.resize(nCoordinates);
    for j=1:nCoordinates
		Q.set(j-1, q2(i,j));
		U.set(j-1, u2(i,j));
    end
	state.setQ(Q);
	state.setU(U);
    
    model.realizeVelocity(state);

    for j=1:nMuscles

        muscle = Millard2012EquilibriumMuscle.safeDownCast(muscles.get(j-1));
%         muscle.set_ignore_activation_dynamics(true); % disable activation dynamics
%         muscle.set_ignore_tendon_compliance(true); % disable tendon compliance

        model.equilibrateMuscles(state);

        FL(i,j)  = muscle.getFiberLength(state);
        FF(i,j)  = muscle.getFiberForce(state);
        
        for k=1:nCoordinates
            coordinate = coordinates.get(k-1);
            coordinate.setValue(state, q2(i,k))
            MA(i,k,j) = muscle.computeMomentArm(state, coordinate);
        end
    end
end

Any guide is greatly appreciated.

Regards,
Mohammadreza

[Thomas Uchida]

- In general, the value of all coordinates must be set before computing moment arms because muscles can span more than one coordinate. Also, when using the Coordinate::setValue() method, you should pass "False" for the third argument when setting all coordinates except the last one (please see topic 14709: viewtopicPhpbb.php?f=91&t=14709).
- The computeMomentArm() method uses the provided state (first argument) to set the pose of the model; the second argument is used to indicate the Coordinate (ModelComponent) with respect to which the moment arm is calculated.

[Mohammadreza Rezaie]

Dear Dr. Uchida,

I appreciate your response. I think the problem was solved. I implemented your suggestion and put it at the beginning of the loop. It seems that there was no need to put joint angles and velocities into state.

Code: Select all

for i=1:frame
    for j=1:nCoordinates
        model.updCoordinateSet().get(j-1).setValue(state, q2(i,j), false)
        model.updCoordinateSet().get(j-1).setSpeedValue(state, u2(i,j))
    end
    model.assemble(state)
    model.realizeVelocity(state);

Do you think getFiberForce works with this method or needs an updated state (by setQ and setU)?

[Thomas Uchida]

Do you think getFiberForce works with this method or needs an updated state (by setQ and setU)?

You are already setting the state when you call setValue() and setSpeedValue(). However, you will need to change realizeVelocity() to realizeDynamics() or higher (https://simtk.org/api_docs/opensim/api_ ... 7def5f54be).

[Mohammadreza Rezaie]

Dear Dr. Uchida,

I really appreciate your help.