def __init__(self, model_path, visualize, integrator_accuracy = 5e-5):
self.integrator_accuracy = integrator_accuracy
self.model = opensim.Model(model_path)
self.model.initSystem()
self.brain = opensim.PrescribedController()
# Enable the visualizer
self.model.setUseVisualizer(visualize)
self.muscleSet = self.model.getMuscles()
self.forceSet = self.model.getForceSet()
self.bodySet = self.model.getBodySet()
self.jointSet = self.model.getJointSet()
self.markerSet = self.model.getMarkerSet()
self.contactGeometrySet = self.model.getContactGeometrySet()
if self.verbose:
self.list_elements()
# Add actuators as constant functions. Then, during simulations
# we will change levels of constants.
# One actuartor per each muscle
for j in range(self.muscleSet.getSize()):
func = opensim.Constant(1.0)
self.brain.addActuator(self.muscleSet.get(j))
self.brain.prescribeControlForActuator(j, func)
self.maxforces.append(self.muscleSet.get(j).getMaxIsometricForce())
self.curforces.append(1.0)
self.noutput = self.muscleSet.getSize()
self.model.addController(self.brain)
self.model.initSystem()
def test_markAdopted2(self):
a = osim.Model()
# We just need the following not to cause a segfault.
# Model add*
pa = osim.PathActuator()
pa.setName('pa')
a.addForce(pa)
probe = osim.Umberger2010MuscleMetabolicsProbe()
probe.setName('probe')
a.addProbe(probe)
ma = osim.MuscleAnalysis()
ma.setName('ma')
a.addAnalysis(ma)
pc = osim.PrescribedController()
pc.setName('pc')
a.addController(pc)
body = osim.Body('body1', 1.0, osim.Vec3(0, 0, 0),
osim.Inertia(0, 0, 0))
loc_in_parent = osim.Vec3(0, 0, 0)
orient_in_parent = osim.Vec3(0, 0, 0)
loc_in_body = osim.Vec3(0, 0, 0)
orient_in_body = osim.Vec3(0, 0, 0)
print "creating Weld Joint.."
joint = osim.WeldJoint("weld_joint", a.getGround(), loc_in_parent,
orient_in_parent, body, loc_in_body,
orient_in_parent)
print "adding a body .."
a.addBody(body)
print "adding a joint .."
a.addJoint(joint)
print "Creating a ConstantDistanceConstraint.."
constr = osim.ConstantDistanceConstraint()
constr.setBody1ByName("ground")
constr.setBody1PointLocation(osim.Vec3(0, 0, 0))
constr.setBody2ByName("body")
constr.setBody2PointLocation(osim.Vec3(1, 0, 0))
constr.setConstantDistance(1)
a.addConstraint(constr)
f = osim.BushingForce("bushing", "ground", "body", osim.Vec3(2, 2, 2),
osim.Vec3(1, 1, 1), osim.Vec3(0, 0, 0),
osim.Vec3(0, 0, 0))
a.addForce(f)
f2 = osim.BushingForce()
a.addForce(f2)
f3 = osim.SpringGeneralizedForce()
a.addForce(f3)
model = osim.Model(os.path.join(test_dir, "arm26.osim"))
g = osim.CoordinateActuator('r_shoulder_elev')
model.addForce(g)
def test(model_path, visualize):
model = opensim.Model(model_path)
brain = opensim.PrescribedController()
model.addController(brain)
state = model.initSystem()
muscleSet = model.getMuscles()
for j in range(muscleSet.getSize()):
brain.addActuator(muscleSet.get(j))
func = opensim.Constant(1.0)
brain.prescribeControlForActuator(j, func)
block = opensim.Body('block', 0.0001, opensim.Vec3(0),
opensim.Inertia(1, 1, .0001, 0, 0, 0))
model.addComponent(block)
pj = opensim.PlanarJoint(
'pin',
model.getGround(), # PhysicalFrame
opensim.Vec3(0, 0, 0),
opensim.Vec3(0, 0, 0),
block, # PhysicalFrame
opensim.Vec3(0, 0, 0),
opensim.Vec3(0, 0, 0))
model.addComponent(pj)
model.initSystem()
pj.getCoordinate(1)
def __init__(self, model_path, k_paths_dict, visualize, integrator_accuracy = 1e-3): # Reduced accuracy for greater speed
self.integrator_accuracy = integrator_accuracy
self.model = opensim.Model(model_path)
self.model.initSystem()
self.brain = opensim.PrescribedController()
self.k_path = k_paths_dict[list(k_paths_dict.keys())[0]]
self.states = pd.read_csv(self.k_path, index_col=False).drop('Unnamed: 0', axis=1)
for speed in list(k_paths_dict.keys()):
self.states_trajectories_dict[speed] = pd.read_csv(k_paths_dict[speed], index_col=False).drop('Unnamed: 0', axis=1)
# Enable the visualizer
self.model.setUseVisualizer(visualize)
self.muscleSet = self.model.getMuscles()
self.forceSet = self.model.getForceSet()
self.bodySet = self.model.getBodySet()
self.jointSet = self.model.getJointSet()
self.markerSet = self.model.getMarkerSet()
self.contactGeometrySet = self.model.getContactGeometrySet()
self.actuatorSet = self.model.getActuators()
if self.verbose:
self.list_elements()
for j in range(self.actuatorSet.getSize()):
func = opensim.Constant(1.0)
self.brain.addActuator(self.actuatorSet.get(j))
self.brain.prescribeControlForActuator(j, func)
self.curforces.append(1.0)
try:
self.maxforces.append(self.muscleSet.get(j).getMaxIsometricForce())
except:
self.maxforces.append(np.inf)
self.noutput = self.actuatorSet.getSize()
self.model.addController(self.brain)
self.model.initSystem()
def test_markAdopted():
a = osim.Model()
# We just need the following not to not cause a segfault.
# Model add*
a.addComponent(osim.PathActuator())
a.addProbe(osim.Umberger2010MuscleMetabolicsProbe())
a.addAnalysis(osim.MuscleAnalysis())
a.addController(osim.PrescribedController())
body = osim.Body('body', 1.0, osim.Vec3(0, 0, 0), osim.Inertia(0, 0, 0))
loc_in_parent = osim.Vec3(0, -0, 0)
orient_in_parent = osim.Vec3(0, 0, 0)
loc_in_body = osim.Vec3(0, 0, 0)
orient_in_body = osim.Vec3(0, 0, 0)
joint = osim.WeldJoint("weld_joint", a.getGroundBody(), loc_in_parent,
orient_in_parent, body, loc_in_body,
orient_in_parent)
a.addBody(body)
constr = osim.ConstantDistanceConstraint()
constr.setBody1ByName("ground")
constr.setBody1PointLocation(osim.Vec3(0, 0, 0))
constr.setBody2ByName("body")
constr.setBody2PointLocation(osim.Vec3(1, 0, 0))
constr.setConstantDistance(1)
a.addConstraint(constr)
# Force requires body names. If not provided, you get a segfault.
f = osim.BushingForce()
f.setBody1ByName("ground")
f.setBody2ByName("body")
a.addForce(f)
model = osim.Model(os.environ['OPENSIM_HOME'] + "/Models/Arm26/arm26.osim")
g = osim.CoordinateActuator('r_shoulder_elev')
model.addForce(g)
def test_PrescribedController_prescribeControlForActuator(self):
# Test memory management for
# PrescribedController::prescribeControlForActuator().
model = osim.Model()
# Body.
body = osim.Body('b1', 1.0, osim.Vec3(0, 0, 0), osim.Inertia(0, 0, 0))
model.addBody(body)
# Joint.
joint = osim.PinJoint('j1', model.getGround(), body)
model.addJoint(joint)
# Actuator.
actu = osim.CoordinateActuator()
actu.setName('actu')
actu.setCoordinate(joint.get_coordinates(0))
model.addForce(actu)
# Controller.
contr = osim.PrescribedController()
contr.addActuator(actu)
self.assertRaises(RuntimeError, contr.prescribeControlForActuator, 1,
osim.Constant(3))
# The following calls should not cause a memory leak:
contr.prescribeControlForActuator(0, osim.Constant(2))
contr.prescribeControlForActuator('actu', osim.Constant(4))
def __init__(self, model_path, visualize):
self.model = opensim.Model(model_path)
self.model.initSystem()
self.brain = opensim.PrescribedController()
# Enable the visualizer
self.model.setUseVisualizer(visualize)
self.muscleSet = self.model.getMuscles()
self.forceSet = self.model.getForceSet()
self.bodySet = self.model.getBodySet()
self.jointSet = self.model.getJointSet()
self.contactGeometrySet = self.model.getContactGeometrySet()
for j in range(self.muscleSet.getSize()):
func = opensim.Constant(1.0)
self.brain.addActuator(self.muscleSet.get(j))
self.brain.prescribeControlForActuator(j, func)
self.maxforces.append(self.muscleSet.get(j).getMaxIsometricForce())
self.curforces.append(1.0)
self.model.addController(self.brain)
biceps = osim.Millard2012EquilibriumMuscle(
"biceps", # Muscle name
200.0, # Max isometric force
0.6, # Optimal fibre length
0.55, # Tendon slack length
0.0) # Pennation angle
biceps.addNewPathPoint("origin", humerus, osim.Vec3(0, 0.8, 0))
biceps.addNewPathPoint("insertion", radius, osim.Vec3(0, 0.7, 0))
# ---------------------------------------------------------------------------
# Add a controller that specifies the excitation of the muscle.
# ---------------------------------------------------------------------------
brain = osim.PrescribedController()
brain.addActuator(biceps)
brain.prescribeControlForActuator("biceps",
osim.StepFunction(0.5, 3.0, 0.3, 1.0))
# ---------------------------------------------------------------------------
# Build model with components created above.
# ---------------------------------------------------------------------------
arm.addBody(humerus)
arm.addBody(radius)
arm.addJoint(shoulder) # Now required in OpenSim4.0
arm.addJoint(elbow)
arm.addForce(biceps)
arm.addController(brain)
def test_markAdoptedSets():
# Set's.
fus = osim.FunctionSet()
fu1 = osim.Constant()
fus.adoptAndAppend(fu1)
del fus
del fu1
gs = osim.GeometrySet()
dg = osim.DisplayGeometry()
gs.adoptAndAppend(dg)
del gs
del dg
s = osim.ScaleSet()
o = osim.Scale()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.BushingForce()
s.adoptAndAppend(o)
del s
del o
cs = osim.ControllerSet()
csc = osim.PrescribedController()
cs.adoptAndAppend(csc)
del cs
del csc
s = osim.ContactGeometrySet()
o = osim.ContactHalfSpace()
s.adoptAndAppend(o)
del s
del o
s = osim.AnalysisSet()
o = osim.MuscleAnalysis()
s.adoptAndAppend(o)
del s
del o
s = osim.ControlSet()
o = osim.ControlLinear()
s.adoptAndAppend(o)
del s
del o
s = osim.MarkerSet()
o = osim.Marker()
s.adoptAndAppend(o)
del s
del o
s = osim.BodySet()
o = osim.Body()
s.adoptAndAppend(o)
del s
del o
s = osim.BodyScaleSet()
o = osim.BodyScale()
s.adoptAndAppend(o)
del s
del o
s = osim.CoordinateSet()
o = osim.Coordinate()
s.adoptAndAppend(o)
del s
del o
s = osim.JointSet()
o = osim.BallJoint()
s.adoptAndAppend(o)
del s
del o
s = osim.PathPointSet()
o = osim.PathPoint()
s.adoptAndAppend(o)
del s
del o
s = osim.IKTaskSet()
o = osim.IKMarkerTask()
s.adoptAndAppend(o)
del s
del o
s = osim.MarkerPairSet()
o = osim.MarkerPair()
s.adoptAndAppend(o)
del s
del o
s = osim.MeasurementSet()
o = osim.Measurement()
s.adoptAndAppend(o)
del s
del o
# TODO
# s = osim.ProbeSet()
# o = osim.Umberger2010MuscleMetabolicsProbe()
# s.adoptAndAppend(o)
# del s
# del o
s = osim.ConstraintSet()
a = osim.Model()
body = osim.Body('body', 1.0, osim.Vec3(0, 0, 0), osim.Inertia(0, 0, 0))
loc_in_parent = osim.Vec3(0, -0, 0)
orient_in_parent = osim.Vec3(0, 0, 0)
loc_in_body = osim.Vec3(0, 0, 0)
orient_in_body = osim.Vec3(0, 0, 0)
joint = osim.WeldJoint("weld_joint", a.getGroundBody(), loc_in_parent,
orient_in_parent, body, loc_in_body,
orient_in_parent)
a.addBody(body)
constr = osim.ConstantDistanceConstraint()
constr.setBody1ByName("ground")
constr.setBody1PointLocation(osim.Vec3(0, 0, 0))
constr.setBody2ByName("body")
constr.setBody2PointLocation(osim.Vec3(1, 0, 0))
constr.setConstantDistance(1)
s.adoptAndAppend(constr)
solution = study.solve()
osim.STOFileAdapter.write(solution.exportToStatesTable(),
"exampleHangingMuscle_states.sto")
osim.STOFileAdapter.write(solution.exportToControlsTable(),
"exampleHangingMuscle_controls.sto")
# Conduct an analysis using MuscleAnalysis and ProbeReporter.
# Create an AnalyzeTool setup file.
analyze = osim.AnalyzeTool()
analyze.setName("analyze")
analyze.setModelFilename("hanging_muscle.osim")
analyze.setStatesFileName("exampleHangingMuscle_states.sto")
analyze.updAnalysisSet().cloneAndAppend(osim.MuscleAnalysis())
analyze.updAnalysisSet().cloneAndAppend(osim.ProbeReporter())
analyze.updControllerSet().cloneAndAppend(
osim.PrescribedController("exampleHangingMuscle_controls.sto"))
analyze.printToXML("exampleHangingMuscle_AnalyzeTool_setup.xml")
# Run the analysis.
analyze = osim.AnalyzeTool("exampleHangingMuscle_AnalyzeTool_setup.xml")
analyze.run()
table_force = osim.TimeSeriesTable(
"analyze_MuscleAnalysis_ActiveFiberForce.sto")
table_velocity = osim.TimeSeriesTable(
"analyze_MuscleAnalysis_FiberVelocity.sto")
time = table_force.getIndependentColumn()
force = table_force.getDependentColumn("muscle").to_numpy()
velocity = table_velocity.getDependentColumn("muscle").to_numpy()
# Plot the terms of the metabolics model, and compare the metabolics model's
# mechanical work rate to the mechanical work rate computed using the
def __init__(self, model_path, visualize, integrator_accuracy = 5e-8, integrator_MaxStepSize = 1e-1, Perturbtime = 50): #Shakiba
self.integrator_accuracy = integrator_accuracy
self.integrator_MaxStepSize = integrator_MaxStepSize #Shakiba
self.model = opensim.Model(model_path)
self.model_state = self.model.initSystem()
self.brain = opensim.PrescribedController()
# Enable the visualizer
self.model.setUseVisualizer(visualize)
self.muscleSet = self.model.getMuscles()
self.forceSet = self.model.getForceSet()
self.bodySet = self.model.getBodySet()
self.jointSet = self.model.getJointSet()
self.markerSet = self.model.getMarkerSet()
self.contactGeometrySet = self.model.getContactGeometrySet()
if self.verbose:
self.list_elements()
# Add actuators as constant functions. Then, during simulations
# we will change levels of constants.
# One actuartor per each muscle
for j in range(self.muscleSet.getSize()):
func = opensim.Constant(1.0)
self.brain.addActuator(self.muscleSet.get(j))
self.brain.prescribeControlForActuator(j, func)
self.maxforces.append(self.muscleSet.get(j).getMaxIsometricForce())
self.curforces.append(1.0)
# Shakiba
# Add external forces as constant functions. Then, during simulations
# we will change levels of constants.
# One actuartor per each ankle
PerturbSites = ['talus_r', 'talus_l'] # perturbation site
external_force = {} # external forces dictionary
for j in PerturbSites:
external_force[j] = opensim.PrescribedForce()
sim_t = 50
sim_dt = self.stepsize
t_pert = np.arange(0, sim_t+sim_dt, sim_dt)
# construct a spline for fx
perturb = opensim.SimmSpline()
sigma = 0.005
miu = Perturbtime
#miu = 8.1
#fx = 0.1*(((1/(sigma*np.sqrt(2*np.pi)))*np.exp(-((t_pert-miu)**2)/(2*sigma**2)))/2) # weighted Gaussian function divided by 2 to account for each leg
fx = 0.5*(((1/(sigma*np.sqrt(2*np.pi)))*np.exp(-((t_pert-miu)**2)/(2*sigma**2)))/2) # weighted Gaussian function divided by 2 to account for each leg
for i in range(t_pert.shape[0]):
perturb.addPoint(t_pert[i], fx[i])
for j in PerturbSites:
#make sure to add the absolute path of the body frame
external_force[j].setBodyName('/bodyset/{}'.format(j))
#define the point of application in body fixed frame
external_force[j].setPointFunctions(opensim.Constant(0),
opensim.Constant(0),
opensim.Constant(0))
#apply external forces
external_force[j].set_forceIsGlobal(True)
external_force[j].setForceFunctions(perturb, opensim.Constant(0), opensim.Constant(0))
self.model.addForce(external_force[j])
#
self.noutput = self.muscleSet.getSize()
self.model.addController(self.brain)
self.model_state = self.model.initSystem()
osimModel.addBody(linkage3)
osimModel.addBody(linkage4)
osimModel.addJoint(tip)
osimModel.addJoint(ankle)
osimModel.addJoint(knee)
osimModel.addJoint(hip)
a1 = addActivationCoordinateActuator(osimModel, "q1", "ap")
a2 = addActivationCoordinateActuator(osimModel, "q2", "kp")
a3 = addActivationCoordinateActuator(osimModel, "q3", "hp")
a_1 = addActivationCoordinateActuator(osimModel, "q1", "am")
a_2 = addActivationCoordinateActuator(osimModel, "q2", "km")
a_3 = addActivationCoordinateActuator(osimModel, "q3", "hm")
actcontroller = osim.PrescribedController()
actcontroller.addActuator(a1)
actcontroller.addActuator(a2)
actcontroller.addActuator(a3)
actcontroller.addActuator(a_1)
actcontroller.addActuator(a_2)
actcontroller.addActuator(a_3)
actcontroller.prescribeControlForActuator("ap", Constant(0))
actcontroller.prescribeControlForActuator("kp", Constant(0))
actcontroller.prescribeControlForActuator("hp", Constant(0))
actcontroller.prescribeControlForActuator("am", Constant(0))
actcontroller.prescribeControlForActuator("km", Constant(0))
actcontroller.prescribeControlForActuator("hm", Constant(0))
actcontroller.set_interpolation_method(3)
osimModel.addController(actcontroller)