def __init__(self, residual_actuator_xml=None):
if residual_actuator_xml:
res_force_set = osim.ForceSet(residual_actuator_xml, True)
n_forces = res_force_set.getSize()
model_force_set = self.model.getForceSet()
for i in range(n_forces):
force = res_force_set.get(i)
model_force_set.cloneAndAppend(force)
def computedMuscleControl():
allDir = list(directories.main(directories))
paramsDir = allDir[1]
subID = allDir[4]
subResultsDir = allDir[5]
ikResultsDir = allDir[6]
idResultsDir = allDir[7]
rraResultsDir = allDir[9]
cmcResultsDir = allDir[10]
# Input Files
idData = idResultsDir + "/subject01_walk1_extLoads.xml"
rraKinematics = rraResultsDir + "/" + "_kinematics_q.sto"
adjustedModel = rraResultsDir + "/" + subID + "_adjustedModel.osim"
# Set XML file Variables
cmcTasks = paramsDir + "/" + "cmcTasks.xml"
cmcActuators = paramsDir + "/" + "cmcActuators.xml"
cmcControlConstraints = paramsDir + "/" + "cmcControlConstraints.xml"
osimGUI = paramsDir + "/" + "osimGUI.xml"
if os.path.exists(cmcResultsDir):
shutil.rmtree(cmcResultsDir, ignore_errors=True)
if not os.path.exists(cmcResultsDir):
os.mkdir(cmcResultsDir)
# Load Model
aModel = osim.Model(adjustedModel)
# initialize system
aModel.initSystem()
cmcTool = osim.CMCTool()
cmcTool.setModel(aModel)
cmcTool.setModelFilename(subID + ".osim")
cmcTool.setDesiredKinematicsFileName(rraKinematics)
cmcTool.setTaskSetFileName(cmcTasks)
cmcTool.setExternalLoadsFileName(idData)
cmcTool.setConstraintsFileName(cmcControlConstraints)
cmcTool.setStartTime(0.8)
cmcTool.setFinalTime(1.2)
cmcTool.setLowpassCutoffFrequency(-1)
cmcTool.setMaxDT(1)
cmcTool.setMinDT(0.0000000001)
cmcTool.setErrorTolerance(0.00001)
# Force Set
myForceSet = osim.ForceSet(aModel, cmcActuators)
cmcTool.setReplaceForceSet(False)
cmcTool.setResultsDir(cmcResultsDir)
# Manually append Force Set
modelForceSet = aModel.updForceSet()
for i in range(myForceSet.getSize()):
aModel.updForceSet().append(myForceSet.get(i))
cmcTool.run()
cmcTool.printToXML(cmcResultsDir + "/" + "cmcSetup.xml")
return ()
def test_markAdoptedSets():
# Set's.
fus = osim.FunctionSet()
fu1 = osim.Constant()
fus.adoptAndAppend(fu1)
del fus
del fu1
s = osim.ScaleSet()
o = osim.Scale()
s.adoptAndAppend(o)
del s
del o
s = osim.ControlSet()
o = osim.ControlLinear()
s.adoptAndAppend(o)
del s
del o
s = osim.BodyScaleSet()
o = osim.BodyScale()
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
s = osim.FrameSet()
o = osim.Body()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.CoordinateLimitForce()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.SpringGeneralizedForce()
s.append(o)
s = osim.ProbeSet()
o = osim.Umberger2010MuscleMetabolicsProbe()
s.adoptAndAppend(o)
del s
del o
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.getGround(),
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)
def run(initial_time, final_time):
"""
inputs
initial time
final time
actuator file = soActuators
kinematics file = subject01_walk1_ik.mot
outputs
"""
import os
import re
import shutil
import opensim as osim
import directories
allDir = list(directories.main(directories))
paramsDir = allDir[1]
subID = allDir[4]
subResultsDir = allDir[5]
ikResultsDir = allDir[6]
idResultsDir = allDir[7]
soResultsDir = allDir[8]
actuatorFile = paramsDir + "/soActuators.xml"
genericSetupSO = paramsDir + "/" + "setupSO.xml"
ikFileName = "subject01_walk1_ik.mot"
ikFile = ikResultsDir + "/" + ikFileName
if os.path.exists(soResultsDir):
shutil.rmtree(soResultsDir, ignore_errors=True)
if not os.path.exists(soResultsDir):
os.mkdir(soResultsDir)
# Load Model
aModel = osim.Model(subResultsDir + "/" + subID + ".osim")
pelvisIndex = aModel.getBodySet().getIndex("pelvis")
pelvisCOM_Vec3 = osim.Vec3()
aModel.getBodySet().get(pelvisIndex).getMassCenter(pelvisCOM_Vec3)
# add reserve actuators
myForceSet = osim.ForceSet(aModel, actuatorFile)
# print(aModel.getForceSet().getSize())
FX = osim.PointActuator.safeDownCast(myForceSet.get(0))
FX.set_point(pelvisCOM_Vec3)
FY = osim.PointActuator.safeDownCast(myForceSet.get(1))
FY.set_point(pelvisCOM_Vec3)
FZ = osim.PointActuator.safeDownCast(myForceSet.get(2))
FZ.set_point(pelvisCOM_Vec3)
for i in range(myForceSet.getSize()):
aModel.updForceSet().append(myForceSet.get(i))
print(aModel.getForceSet().getSize())
# initialize system
aModel.initSystem()
# Initialize External Loads File from Generic File
extLoads = idResultsDir + "/subject01_walk1_extLoads.xml"
# Get .mot data to determine time range
# motCoordsData = osim.Storage(ikFile)
# Get initial and final time
# initial_time = motCoordsData.getFirstTime()
# final_time = motCoordsData.getLastTime()
# Analyze Tool Setup
analyzeTool = osim.AnalyzeTool(genericSetupSO)
analyzeTool.setInitialTime(initial_time)
analyzeTool.setFinalTime(final_time)
analyzeTool.setResultsDir(soResultsDir)
analyzeTool.setModelFilename("")
analyzeTool.setName(re.sub('_ik.mot', '', ikFileName))
myForceSetArray = analyzeTool.getForceSetFiles()
myForceSetArray.set(0, "")
analyzeTool.setReplaceForceSet(False)
analyzeTool.setForceSetFiles(myForceSetArray)
# Set coordinates
coordtype = "mot"
if coordtype == "mot":
analyzeTool.setStatesFileName("")
analyzeTool.setCoordinatesFileName(ikFile)
elif coordtype == "states":
analyzeTool.setStatesFileName(ikFile)
analyzeTool.setCoordinatesFileName("")
analyzeTool.setExternalLoadsFileName(extLoads)
analyzeTool.setModel(aModel)
analyzeTool.run()
analyzeTool.printToXML(soResultsDir + "/" +
re.sub('ik.mot', 'outSetupSO.xml', ikFileName))
aModel.printToXML(soResultsDir + "/" + subID + "_soActuators.osim")
os.system('cls' if os.name == 'nt' else 'clear')
return ()
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)
def perform_so(model_file, ik_file, grf_file, grf_xml, reserve_actuators,
results_dir):
"""Performs Static Optimization using OpenSim.
Parameters
----------
model_file: str
OpenSim model (.osim)
ik_file: str
kinematics calculated from Inverse Kinematics
grf_file: str
the ground reaction forces
grf_xml: str
xml description containing how to apply the GRF forces
reserve_actuators: str
path to the reserve actuator .xml file
results_dir: str
directory to store the results
"""
# model
model = opensim.Model(model_file)
# prepare external forces xml file
name = os.path.basename(grf_file)[:-8]
external_loads = opensim.ExternalLoads(model, grf_xml)
external_loads.setExternalLoadsModelKinematicsFileName(ik_file)
external_loads.setDataFileName(grf_file)
external_loads.setLowpassCutoffFrequencyForLoadKinematics(6)
external_loads.printToXML(results_dir + name + '.xml')
# add reserve actuators
force_set = opensim.ForceSet(model, reserve_actuators)
force_set.setMemoryOwner(False) # model will be the owner
for i in range(0, force_set.getSize()):
model.updForceSet().append(force_set.get(i))
# construct static optimization
motion = opensim.Storage(ik_file)
static_optimization = opensim.StaticOptimization()
static_optimization.setStartTime(motion.getFirstTime())
static_optimization.setEndTime(motion.getLastTime())
static_optimization.setUseModelForceSet(True)
static_optimization.setUseMusclePhysiology(True)
static_optimization.setActivationExponent(2)
static_optimization.setConvergenceCriterion(0.0001)
static_optimization.setMaxIterations(100)
model.addAnalysis(static_optimization)
# analysis
analysis = opensim.AnalyzeTool(model)
analysis.setName(name)
analysis.setModel(model)
analysis.setInitialTime(motion.getFirstTime())
analysis.setFinalTime(motion.getLastTime())
analysis.setLowpassCutoffFrequency(6)
analysis.setCoordinatesFileName(ik_file)
analysis.setExternalLoadsFileName(results_dir + name + '.xml')
analysis.setLoadModelAndInput(True)
analysis.setResultsDir(results_dir)
analysis.run()
so_force_file = results_dir + name + '_StaticOptimization_force.sto'
so_activations_file = results_dir + name + \
'_StaticOptimization_activation.sto'
return (so_force_file, so_activations_file)
def reduceResidualActuators():
allDir = list(directories.main(directories))
paramsDir = allDir[1]
subID = allDir[4]
subResultsDir = allDir[5]
ikResultsDir = allDir[6]
idResultsDir = allDir[7]
rraResultsDir = allDir[9]
# Input Files
idData = idResultsDir + "/subject01_walk1_extLoads.xml"
ikFileName = "subject01_walk1_ik.mot"
ikFile = ikResultsDir + "/" + ikFileName
# Set XML file Variables
RRATasks = paramsDir + "/" + "RRATasks.xml"
RRAActuatorsFile = paramsDir + "/" + "RRAActuators.xml"
RRAActuators = "RRAActuators.xml"
if os.path.exists(rraResultsDir):
shutil.rmtree(rraResultsDir, ignore_errors=True)
if not os.path.exists(rraResultsDir):
os.mkdir(rraResultsDir)
# Load Model
aModel = osim.Model(subResultsDir + "/" + subID + ".osim")
# initialize system
aModel.initSystem()
rraTool = osim.RRATool()
rraTool.setModel(aModel)
rraTool.setModelFilename(subID + ".osim")
rraTool.setDesiredKinematicsFileName(ikFile)
rraTool.setTaskSetFileName(RRATasks)
rraTool.setExternalLoadsFileName(idData)
rraTool.setStartTime(0.5)
rraTool.setFinalTime(1.5)
rraTool.setLowpassCutoffFrequency(6)
# Force Set
myForceSet = osim.ForceSet(aModel, RRAActuatorsFile)
rraTool.setReplaceForceSet(False)
shutil.copy(RRAActuatorsFile, rraResultsDir + "/" + RRAActuators)
rraTool.setAdjustCOMToReduceResiduals(True)
rraTool.setAdjustedCOMBody("torso")
rraTool.setResultsDir(rraResultsDir)
rraTool.setOutputModelFileName(rraResultsDir + "/" + subID +
"_adjustedModel.osim")
# Manually Replace Force Set
modelForceSet = aModel.updForceSet()
modelMuscles = osim.ForceSet(aModel.getForceSet())
modelForceSet.clearAndDestroy()
for i in range(myForceSet.getSize()):
aModel.updForceSet().append(myForceSet.get(i))
rraTool.run()
rraTool.printToXML(rraResultsDir + "/" + "rraSetup.xml")
rraModel = osim.Model(rraResultsDir + "/" + subID + "_adjustedModel.osim")
rraModel.setName(subID + "_adjustedModel")
rraModel.updForceSet().clearAndDestroy()
for i in range(modelMuscles.getSize()):
rraModel.updForceSet().append(modelMuscles.get(i))
rraModel.printToXML(rraResultsDir + "/" + subID + "_adjustedModel.osim")
return ()
def __init__(self, external_load_xml=None):
if external_load_xml:
force_set = osim.ForceSet(external_load_xml)
n_forces = force_set.getSize()
for i in range(n_forces):
self.model.getForceSet().append(force_set.get(i))
def replace_thelen_muscles_with_millard(model_file, target_folder):
"""Replaces Thelen muscles with Millard muscles so that we can disable
tendon compliance and perform MuscleAnalysis to compute normalized
fiber length/velocity without spikes.
"""
model = opensim.Model(model_file)
new_force_set = opensim.ForceSet()
force_set = model.getForceSet()
for i in range(force_set.getSize()):
force = force_set.get(i)
muscle = opensim.Muscle.safeDownCast(force)
millard_muscle = opensim.Millard2012EquilibriumMuscle.safeDownCast(
force)
thelen_muscle = opensim.Thelen2003Muscle.safeDownCast(force)
if muscle is None:
new_force_set.adoptAndAppend(force.clone())
elif millard_muscle is not None:
millard_muscle = millard_muscle.clone()
millard_muscle.set_ignore_tendon_compliance(True)
new_force_set.adoptAndAppend(millard_muscle)
elif thelen_muscle is not None:
millard_muscle = opensim.Millard2012EquilibriumMuscle()
# properties
millard_muscle.set_default_activation(
thelen_muscle.getDefaultActivation())
millard_muscle.set_activation_time_constant(
thelen_muscle.get_activation_time_constant())
millard_muscle.set_deactivation_time_constant(
thelen_muscle.get_deactivation_time_constant())
# millard_muscle.set_fiber_damping(0)
# millard_muscle.set_tendon_strain_at_one_norm_force(
# thelen_muscle.get_FmaxTendonStrain())
millard_muscle.setName(thelen_muscle.getName())
millard_muscle.set_appliesForce(thelen_muscle.get_appliesForce())
millard_muscle.setMinControl(thelen_muscle.getMinControl())
millard_muscle.setMaxControl(thelen_muscle.getMaxControl())
millard_muscle.setMaxIsometricForce(
thelen_muscle.getMaxIsometricForce())
millard_muscle.setOptimalFiberLength(
thelen_muscle.getOptimalFiberLength())
millard_muscle.setTendonSlackLength(
thelen_muscle.getTendonSlackLength())
millard_muscle.setPennationAngleAtOptimalFiberLength(
thelen_muscle.getPennationAngleAtOptimalFiberLength())
millard_muscle.setMaxContractionVelocity(
thelen_muscle.getMaxContractionVelocity())
# millard_muscle.set_ignore_tendon_compliance(
# thelen_muscle.get_ignore_tendon_compliance())
millard_muscle.set_ignore_tendon_compliance(True)
millard_muscle.set_ignore_activation_dynamics(
thelen_muscle.get_ignore_activation_dynamics())
# muscle path
pathPointSet = thelen_muscle.getGeometryPath().getPathPointSet()
geomPath = millard_muscle.updGeometryPath()
for j in range(pathPointSet.getSize()):
pathPoint = pathPointSet.get(j).clone()
geomPath.updPathPointSet().adoptAndAppend(pathPoint)
# append
new_force_set.adoptAndAppend(millard_muscle)
else:
raise RuntimeError('cannot handle the type of muscle: ' +
force.getName())
new_force_set.printToXML(os.path.join(target_folder, 'muscle_set.xml'))