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197 lines (160 loc) · 8.42 KB
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function makeSimulation(trial)
curDirWithMatlabScripts = fileparts(mfilename('fullpath'));
cd([curDirWithMatlabScripts,'/..']);
simulationHomeDir = cd;
if strcmpi(trial, 'walk')
makeSimulation_walk(simulationHomeDir);
elseif strcmpi(trial, 'run')
makeSimulation_run(simulationHomeDir);
else
warning('fx input must be ''walk'' or ''run''; generating running simulation')
makeSimulation_run(simulationHomeDir);
end
cd(curDirWithMatlabScripts);
end
function makeSimulation_walk(simulationHomeDir)
import org.opensim.modeling.*
disp('walk')
% Scale
cd([simulationHomeDir,'/Scale'])
system('scale -S scale_setup_walk_scaleOnly.xml');
system('scale -S scale_setup_walk.xml');
% IK
cd([simulationHomeDir,'/IK'])
system('ik -S ik_setup_walk.xml');
% RRA
cd([simulationHomeDir,'/RRA/walk']);
system('rra -S rra_setup_walk_1.xml');
outlog = fileread('out.log');
massChange = str2double(outlog(regexpi(outlog, 'total mass change: ', 'end'):regexpi(outlog, 'total mass change: .?[0-9]+[.][0-9]+', 'end')));
disp(['walk, rra 1, dMass = ', num2str(massChange)])
dCOM = outlog(regexpi(outlog, 'Mass Center \(COM\) adjustment:', 'end'):regexpi(outlog, 'Mass Center \(COM\) adjustment: .+]', 'end'));
disp(['walk, rra 1, dCOM = ', dCOM])
osimModel_rraMassChanges = Model('subject_walk_rra1.osim');
osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel_rraMassChanges, massChange);
osimModel_rraMassChanges.print('subject_walk_rra1.osim');
system('rra -S rra_setup_walk_2.xml');
outlog = fileread('out.log');
massChange = str2double(outlog(regexpi(outlog, 'total mass change: ', 'end'):regexpi(outlog, 'total mass change: .?[0-9]+[.][0-9]+', 'end')));
disp(['walk, rra 2, dMass = ', num2str(massChange)])
dCOM = outlog(regexpi(outlog, 'Mass Center \(COM\) adjustment:', 'end'):regexpi(outlog, 'Mass Center \(COM\) adjustment: .+]', 'end'));
disp(['walk, rra 2, dCOM = ', dCOM])
osimModel_rraMassChanges = Model('subject_walk_rra2.osim');
osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel_rraMassChanges, massChange);
osimModel_rraMassChanges.print('subject_walk_rra2.osim');
% Scale muscle forces based on final mass, set vmax
osimModel_postRRA = scaleOptimalForceSubjectSpecific(osimModel_rraMassChanges, osimModel_rraMassChanges, 1.70, 1.83);
osimModel_postRRA = setMaxContractionVelocityAllMuscles(osimModel_postRRA, 15.0);
osimModel_postRRA.print([simulationHomeDir,'/CMC/walk/subject_walk_adjusted.osim']);
% CMC
cd([simulationHomeDir,'/CMC/walk']);
system('cmc -S cmc_setup_walk.xml');
% ID
cd([simulationHomeDir,'/ID']);
system('id -S id_setup_walk.xml');
end
function makeSimulation_run(simulationHomeDir)
import org.opensim.modeling.*
disp('run')
% Scale
cd([simulationHomeDir,'/Scale'])
system('scale -S scale_setup_run.xml');
% IK
cd([simulationHomeDir,'/IK'])
system('ik -S ik_setup_run.xml');
% RRA
cd([simulationHomeDir,'/RRA/run']);
system('rra -S rra_setup_run_1.xml');
outlog = fileread('out.log');
massChange = str2double(outlog(regexpi(outlog, 'total mass change: ', 'end'):regexpi(outlog, 'total mass change: .?[0-9]+[.][0-9]+', 'end')));
disp(['run, rra 1, dMass = ', num2str(massChange)])
dCOM = outlog(regexpi(outlog, 'Mass Center \(COM\) adjustment:', 'end'):regexpi(outlog, 'Mass Center \(COM\) adjustment: .+]', 'end'));
disp(['run, rra 1, dCOM = ', dCOM])
osimModel_rraMassChanges = Model('subject_run_rra1.osim');
osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel_rraMassChanges, massChange);
osimModel_rraMassChanges.print('subject_run_rra1.osim');
system('rra -S rra_setup_run_2.xml');
outlog = fileread('out.log');
massChange = str2double(outlog(regexpi(outlog, 'total mass change: ', 'end'):regexpi(outlog, 'total mass change: .?[0-9]+[.][0-9]+', 'end')));
disp(['run, rra 2, dMass = ', num2str(massChange)])
dCOM = outlog(regexpi(outlog, 'Mass Center \(COM\) adjustment:', 'end'):regexpi(outlog, 'Mass Center \(COM\) adjustment: .+]', 'end'));
disp(['run, rra 2, dCOM = ', dCOM])
osimModel_rraMassChanges = Model('subject_run_rra2.osim');
osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel_rraMassChanges, massChange);
osimModel_rraMassChanges.print('subject_run_rra2.osim');
system('rra -S rra_setup_run_3.xml');
outlog = fileread('out.log');
massChange = str2double(outlog(regexpi(outlog, 'total mass change: ', 'end'):regexpi(outlog, 'total mass change: .?[0-9]+[.][0-9]+', 'end')));
disp(['run, rra 3, dMass = ', num2str(massChange)])
dCOM = outlog(regexpi(outlog, 'Mass Center \(COM\) adjustment:', 'end'):regexpi(outlog, 'Mass Center \(COM\) adjustment: .+]', 'end'));
disp(['run, rra 3, dCOM = ', dCOM])
osimModel_rraMassChanges = Model('subject_run_rra3.osim');
osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel_rraMassChanges, massChange);
osimModel_rraMassChanges.print('subject_run_rra3.osim');
% Scale muscle forces based on final mass, set vmax
osimModel_postRRA = scaleOptimalForceSubjectSpecific(osimModel_rraMassChanges, osimModel_rraMassChanges, 1.70, 1.78);
osimModel_postRRA = setMaxContractionVelocityAllMuscles(osimModel_postRRA, 15.0);
osimModel_postRRA.print([simulationHomeDir,'/CMC/run/subject_run_adjusted.osim']);
% CMC
cd([simulationHomeDir,'/CMC/run']);
system('cmc -S cmc_setup_run.xml');
% ID
cd([simulationHomeDir,'/ID']);
system('id -S id_setup_run.xml');
end
function osimModel_scaledForces = scaleOptimalForceSubjectSpecific(osimModel_generic, osimModel_scaled, height_generic, height_scaled)
mass_generic = getMassOfModel(osimModel_generic);
mass_scaled = getMassOfModel(osimModel_scaled);
Vtotal_generic = 47.05 * mass_generic * height_generic + 1289.6;
Vtotal_scaled = 47.05 * mass_scaled * height_scaled + 1289.6;
allMuscles_generic = osimModel_generic.getMuscles();
allMuscles_scaled = osimModel_scaled.getMuscles();
for i=0:allMuscles_generic.getSize()-1
currentMuscle_generic = allMuscles_generic.get(i);
currentMuscle_scaled = allMuscles_scaled.get(i);
lmo_generic = currentMuscle_generic.getOptimalFiberLength();
lmo_scaled = currentMuscle_scaled.getOptimalFiberLength();
forceScaleFactor = (Vtotal_scaled/Vtotal_generic)/(lmo_scaled/lmo_generic);
currentMuscle_scaled.setMaxIsometricForce( forceScaleFactor * currentMuscle_generic.getMaxIsometricForce() );
end
osimModel_scaledForces = osimModel_scaled;
end
function osimModel_scaledForces = scaleOptimalForce_constant(osimModel_generic, osimModel_scaled, scaleFactor)
allMuscles_generic = osimModel_generic.getMuscles();
allMuscles_scaled = osimModel_scaled.getMuscles();
for i=0:allMuscles_generic.getSize()-1
currentMuscle_generic = allMuscles_generic.get(i);
currentMuscle_scaled = allMuscles_scaled.get(i);
currentMuscle_scaled.setMaxIsometricForce( scaleFactor * currentMuscle_generic.getMaxIsometricForce() );
end
osimModel_scaledForces = osimModel_scaled;
end
function osimModel_rraMassChanges = setMassOfBodiesUsingRRAMassChange(osimModel, massChange)
currTotalMass = getMassOfModel(osimModel);
suggestedNewTotalMass = currTotalMass + massChange;
massScaleFactor = suggestedNewTotalMass/currTotalMass;
allBodies = osimModel.getBodySet();
for i = 0:allBodies.getSize()-1
currBodyMass = allBodies.get(i).getMass();
newBodyMass = currBodyMass*massScaleFactor;
allBodies.get(i).setMass(newBodyMass);
end
osimModel_rraMassChanges = osimModel;
end
function totalMass = getMassOfModel(osimModel)
totalMass = 0;
allBodies = osimModel.getBodySet();
for i=0:allBodies.getSize()-1
curBody = allBodies.get(i);
totalMass = totalMass + curBody.getMass();
end
end
function osimModel_vmax = setMaxContractionVelocityAllMuscles(osimModel, maxContractionVelocity)
Muscles = osimModel.getMuscles();
numMuscles = Muscles.getSize();
for i = 0:numMuscles-1
currentMuscle = Muscles.get(i);
currentMuscle.setMaxContractionVelocity(maxContractionVelocity);
end
osimModel_vmax = osimModel;
end