def generate_results(self, root_dir, args):
self.parse_args(args)
from transform_and_filter_ground_reaction import \
transform_and_filter_ground_reaction
# TODO: We aren't actually using this filtered file yet.
transform_and_filter_ground_reaction(
os.path.join(root_dir, 'resources/Rajagopal2016/emg_walk_raw.anc'),
os.path.join(root_dir, 'resources/Rajagopal2016/grf_walk.mot'),
'ground_reaction_forces',
'rlr',
mode='multicutoff')
modelProcessor = self.create_model_processor(root_dir)
cmc = osim.CMCTool(
os.path.join(root_dir,
'code/motion_prescribed_walking_cmc_setup.xml'))
analyze = osim.AnalyzeTool(
os.path.join(root_dir,
'code/motion_prescribed_walking_analyze_setup.xml'))
# 2.5 minute
if self.cmc:
cmc.run()
analyze.run()
mesh_interval = (self.final_time - self.initial_time) / 25.0
# 8 minutes
if self.inverse:
solution_filepath = self.mocoinverse_solution_file % root_dir
self.solve_inverse(root_dir, modelProcessor, mesh_interval,
solution_filepath)
# TODO
# # 0.04 and 0.03 work
# inverse.set_mesh_interval(0.01)
# # inverse.set_convergence_tolerance(1e-4)
# solution = inverse.solve()
# solution.getMocoSolution().write(self.mocoinverse_fine_solution_file % root_dir)
# MocoInverse, minimize joint reactions
# -------------------------------------
inverse = self.create_inverse(root_dir, modelProcessor, mesh_interval)
study = inverse.initialize()
problem = study.updProblem()
reaction_r = osim.MocoJointReactionGoal('reaction_r', 0.005)
reaction_r.setJointPath('/jointset/walker_knee_r')
reaction_r.setReactionMeasures(['force-x', 'force-y'])
reaction_l = osim.MocoJointReactionGoal('reaction_l', 0.005)
reaction_l.setJointPath('/jointset/walker_knee_l')
reaction_l.setReactionMeasures(['force-x', 'force-y'])
problem.addGoal(reaction_r)
problem.addGoal(reaction_l)
solver = osim.MocoCasADiSolver.safeDownCast(study.updSolver())
# 13 minutes.
if self.knee:
solution_reaction = study.solve()
solution_reaction.write(self.mocoinverse_jointreaction_solution_file % root_dir)
def getStepStatistics(results_folder, force_threshold = 10, minimum_step_time = 0.5):
# find states file and model file
for fname in os.listdir(results_folder):
if fname.endswith('states.sto'):
states_file = os.path.join(results_folder, fname)
for fname in os.listdir(results_folder):
if fname.endswith('.osim'):
model_file = os.path.join(results_folder, fname)
# get ground contact information from HuntCrossleyForce's
model = opensim.Model(model_file)
states = opensim.States(states_file)
analyzeTool = opensim.AnalyzeTool()
analyzeTool.setModel(model)
analyzeTool.setStates(states)
left_foot_forces = opensim.getForce('foot_l').getOutput() #<HuntCrossleyForce name="foot_l">
right_foot_forces = opensim.getForce('foot_r').getOutput() #<HuntCrossleyForce name="foot_r">
analyzeTool.add(leftFootForces)
analyzeTool.add(rightFootForces)
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 setup_muscle_analysis_xml(trial: str, model: str, directory: str,
time_range: list, cut_off_freq: np.float64):
'''
NOTE: Any attribute not changed within this function must be changed in the original template
file
Inputs: trial: trial name, e.g., "_12Mar_ss_12ms_01"
model: model name, e.g., "AB08"
directory: output directory name
time_range: start and end times
cuf_off_frequency: low pass cut-off frequency
'''
# Get analyze tool
analyze_tool = osim.AnalyzeTool()
# Set tool name
new_analyze_tool_name = model + trial
analyze_tool.setName(new_analyze_tool_name)
# Set the opensim model name
analyze_tool.setModelFilename(directory + "\\" + model + "\\" + model +
".osim")
# Set the results directory
analyze_tool.setResultsDir(directory + "\\" + model + "\\" + trial)
# Set the external loads file
external_loads_file = directory + "\\" + model + "\\" + trial + "\\" + trial + 'ExternalLoads.xml'
analyze_tool.setExternalLoadsFileName(external_loads_file)
# Set the coordinates file
coord_file = directory + "\\" + model + "\\" + trial + "\\" + trial + 'IKResults.mot'
analyze_tool.setCoordinatesFileName(coord_file)
# Set low pass cut-off frequency, NOTE: Must be a double (np.float64)
analyze_tool.setLowpassCutoffFrequency(np.float64(cut_off_freq))
# Set the time range, NOTE: Must be a double (np.float64)
analyze_tool.setInitialTime(np.float64(time_range[0]))
analyze_tool.setFinalTime(np.float64(time_range[-1]))
''' Add muscle analysis '''
analysis_set = analyze_tool.getAnalysisSet()
muscle_analysis = osim.MuscleAnalysis()
muscle_analysis.setStartTime(np.float64(time_range[0]))
muscle_analysis.setEndTime(np.float64(time_range[-1]))
muscle_analysis.setComputeMoments(
True) # Bug, this is not being set to true in the xml file
analysis_set.cloneAndAppend(muscle_analysis)
''' Write file '''
xml_setup_path = directory + "\\" + model + "\\" + trial + "\\" + trial + "MuscleAnalysisSetup.xml"
analyze_tool.printToXML(xml_setup_path)
''' Temporary fix to set compute moments to true and to remove numerical inaccuracy in times '''
dom = minidom.parse(xml_setup_path)
analysis_set = dom.getElementsByTagName("AnalysisSet")
analysis_set_child = analysis_set.item(0)
objects_set = analysis_set_child.getElementsByTagName("objects")
objects_set_child = objects_set.item(0)
muscle_analysis = objects_set_child.getElementsByTagName("MuscleAnalysis")
muscle_analysis_child = muscle_analysis.item(0)
muscle_analysis_child.getElementsByTagName(
"compute_moments")[0].firstChild.nodeValue = "true"
dom.getElementsByTagName("initial_time")[0].firstChild.nodeValue = round(
time_range[0], 3)
dom.getElementsByTagName("final_time")[0].firstChild.nodeValue = round(
time_range[-1], 3)
muscle_analysis_child.getElementsByTagName(
"start_time")[0].firstChild.nodeValue = round(time_range[0], 3)
muscle_analysis_child.getElementsByTagName(
"end_time")[0].firstChild.nodeValue = round(time_range[-1], 3)
with open(xml_setup_path, 'w') as xml_file:
dom.writexml(xml_file, addindent='\t', newl='\n', encoding='UTF-8')
def perform_jra(model_file,
ik_file,
grf_file,
grf_xml,
reserve_actuators,
muscle_forces_file,
results_dir,
prefix=''):
"""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
muscle_forces_file: str
path to the file containing the muscle forces from SO
results_dir: str
directory to store the results
prefix: str
prefix of the resultant joint reaction loads
"""
# 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')
# TODO this may not be needed
# add reserve actuators (must not be appended when performing JRA)
# 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))
# # model.addForce(force_set.get(i))
# construct joint reaction analysis
motion = opensim.Storage(ik_file)
joint_reaction = opensim.JointReaction(model)
joint_reaction.setName('JointReaction')
joint_reaction.setStartTime(motion.getFirstTime())
joint_reaction.setEndTime(motion.getLastTime())
joint_reaction.setForcesFileName(muscle_forces_file)
model.addAnalysis(joint_reaction)
model.initSystem()
# analysis
analysis = opensim.AnalyzeTool(model)
analysis.setName(prefix + name)
analysis.setModel(model)
analysis.setModelFilename(model_file)
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()
jra_file = results_dir + name + '_JointReaction_ReactionLoads.sto'
return jra_file
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)
solver = study.initCasADiSolver()
solver.set_num_mesh_intervals(25)
solver.set_multibody_dynamics_mode("implicit")
solver.set_optim_convergence_tolerance(1e-4)
solver.set_optim_constraint_tolerance(1e-4)
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(
def run(setup, resultsDirectory):
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]
# cmcResultsDir = allDir[10]
# jrResultsDir = allDir[11]
# # actuatorFile = paramsDir + "/soActuators.xml"
# # genericSetupSO = paramsDir + "/" + "setupSO.xml"
# ikFileName = "subject01_walk1_ik.mot"
# ikFile = ikResultsDir + "/" + ikFileName
# # soForces = soResultsDir + "/" + "subject01_walk1_StaticOptimization_force.sto"
# if os.path.exists(jrResultsDir):
# shutil.rmtree(jrResultsDir, ignore_errors=True)
# if not os.path.exists(jrResultsDir):
# os.mkdir(jrResultsDir)
# # Load Model
aModel = osim.Model(subResultsDir + "/" + subID + ".osim")
# # 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 for Static Optimization
analyzeTool = osim.AnalyzeTool(setup)
analyzeTool.setModel(aModel)
analyzeTool.setResultsDir(resultsDirectory)
analyzeTool.run()
# analyzeTool = osim.AnalyzeTool(cmcJrSetup)
# analyzeTool.setExternalLoadsFileName(extLoads)
# analyzeTool.setInitialTime(initial_time)
# analyzeTool.setFinalTime(final_time)
# analyzeTool.setLowpassCutoffFrequency(6)
# analyzeTool.setOutputPrecision(20)
# myForceSet = osim.ForceSet(aModel, actuatorFile)
# for i in range(myForceSet.getSize()):
# aModel.updForceSet().append(myForceSet.get(i))
# print(aModel.getForceSet().getSize())
# analysisSet = analyzeTool.getAnalysisSet()
# myForceSetArray = analyzeTool.getForceSetFiles()
# myForceSetArray.set(0, "")
# analyzeTool.setReplaceForceSet(False)
# analyzeTool.setForceSetFiles(myForceSetArray)
# # Joint Reaction Analysis
# jrTool = osim.JointReaction(jrSetup)
# analysisSet.cloneAndAppend(jrTool)
# # Set coordinates
# coordtype = "mot"
# if coordtype == "mot":
# analyzeTool.setStatesFileName("")
# analyzeTool.setCoordinatesFileName(ikFile)
# elif coordtype == "states":
# analyzeTool.setStatesFileName(ikFile)
# analyzeTool.setCoordinatesFileName("")
# analyzeTool.verifyControlsStates()
# analyzeTool.setResultsDir(jrResultsDir)
# # analyzeTool.printToXML(paramsDir +"/setupJR.xml")
# analyzeTool.run()
return ()
os.system('cls' if os.name == 'nt' else 'clear')
def run_analyze_tool(self, trial):
if self.prefix and not trial.stem.startswith(self.prefix):
# skip file if user specified a prefix and prefix is not present in current file
pass
else:
print(f"\t{trial.stem}")
# model
model = osim.Model(self.model_input) if isinstance(self.model_input, str) is True else self.model_input
model.initSystem()
# get starting and ending time
motion = osim.Storage(f"{trial.resolve()}")
first_time = motion.getFirstTime()
last_time = motion.getLastTime()
# prepare external forces xml file
if self.xml_forces:
external_loads = osim.ExternalLoads(self.xml_forces, True)
if self.prefix:
external_loads.setDataFileName(
f"{Path(self.ext_forces_dir, trial.stem.replace(f'{self.prefix}_', '')).resolve()}.sto"
)
else:
external_loads.setDataFileName(
f"{Path(self.ext_forces_dir, trial.stem).resolve()}.sto"
)
external_loads.setExternalLoadsModelKinematicsFileName(
f"{trial.resolve()}"
)
if self.low_pass:
external_loads.setLowpassCutoffFrequencyForLoadKinematics(
self.low_pass
)
temp_xml = Path(f"{trial.stem}_temp.xml")
external_loads.printToXML(f"{temp_xml.resolve()}") # temporary xml file
current_class = self.get_class_name()
params = self.parse_analyze_set_xml(self.xml_input, node=current_class)
solve_for_equilibrium = False
if current_class == "StaticOptimization":
analysis = osim.StaticOptimization(model)
analysis.setUseModelForceSet(params["use_model_force_set"])
analysis.setActivationExponent(params["activation_exponent"])
analysis.setUseMusclePhysiology(params["use_muscle_physiology"])
analysis.setConvergenceCriterion(
params["optimizer_convergence_criterion"]
)
analysis.setMaxIterations(int(params["optimizer_max_iterations"]))
elif current_class == "MuscleAnalysis":
solve_for_equilibrium = True
analysis = osim.MuscleAnalysis(model)
coord = osim.ArrayStr()
for c in params["moment_arm_coordinate_list"]:
coord.append(c)
analysis.setCoordinates(coord)
mus = osim.ArrayStr()
for m in params["muscle_list"]:
mus.append(m)
analysis.setMuscles(mus)
# analysis.setComputeMoments(params["compute_moments"])
elif current_class == "JointReaction":
# construct joint reaction analysis
analysis = osim.JointReaction(model)
if params["forces_file"] or self.forces_file:
force_file = self.forces_file if self.forces_file else params["forces_file"]
analysis.setForcesFileName(force_file)
joint = osim.ArrayStr()
for j in params["joint_names"]:
joint.append(j)
analysis.setJointNames(joint)
body = osim.ArrayStr()
for b in params["apply_on_bodies"]:
body.append(b)
analysis.setOnBody(body)
frame = osim.ArrayStr()
for f in params["express_in_frame"]:
frame.append(f)
analysis.setInFrame(frame)
else:
raise ValueError("AnalyzeTool must be called from a child class")
analysis.setModel(model)
analysis.setName(current_class)
analysis.setOn(params["on"])
analysis.setStepInterval(int(params["step_interval"]))
analysis.setInDegrees(params["in_degrees"])
analysis.setStartTime(first_time)
analysis.setEndTime(last_time)
model.addAnalysis(analysis)
if self.print_to_xml is True:
analysis.printToXML(f"{self.xml_output}/{current_class}_analysis.xml")
# analysis tool
analyze_tool = osim.AnalyzeTool(model)
analyze_tool.setName(trial.stem)
analyze_tool.setModel(model)
analyze_tool.setModelFilename(Path(model.toString()).stem)
analyze_tool.setSolveForEquilibrium(solve_for_equilibrium)
if self.xml_actuators:
force_set = osim.ArrayStr()
force_set.append(self.xml_actuators)
analyze_tool.setForceSetFiles(force_set)
analyze_tool.updateModelForces(model, self.xml_actuators)
analyze_tool.setInitialTime(first_time)
analyze_tool.setFinalTime(last_time)
if self.low_pass:
analyze_tool.setLowpassCutoffFrequency(self.low_pass)
analyze_tool.setCoordinatesFileName(f"{trial.resolve()}")
if self.xml_forces:
analyze_tool.setExternalLoadsFileName(f"{temp_xml}")
analyze_tool.setLoadModelAndInput(True)
analyze_tool.setResultsDir(f"{self.sto_output}")
analyze_tool.run()
if self.xml_forces:
temp_xml.unlink() # delete temporary xml file
if self.remove_empty_files:
self._remove_empty_files(directory=self.sto_output)
if self.contains:
self._subset_output(directory=self.sto_output, contains=self.contains)
def run_static_optimization(so_file):
# model = osim.Model(model_path)
tool = osim.AnalyzeTool(so_file)
# # model t and r coordinates have to be locked
tool.run()
import opensim as osim
modelFilename = 'Model/Driving.osim'
actuatorFilename = 'Actuator/Actuators_upper_limb.xml'
settingFile = 'so.xml'
resultDir = 'Result'
#Subject file list
subjectList = ['SubUnknown']
#External force list
exforceList = [220, 260]
#Motion file list
motList = [30, -30]
model = osim.Model(modelFilename)
model.initSystem()
aTool = osim.AnalyzeTool()
##Set actuator (Optional)
actuatorSet = osim.ArrayStr()
actuatorSet.append(actuatorFilename)
aTool.setForceSetFiles(actuatorSet)
##Set the directory for the result
aTool.setResultsDir(resultDir)
##Set the condition of SO
aSet = aTool.getAnalysisSet()
so = osim.StaticOptimization()
so.setName('StaticOptimization')
aSet.insert(0, so)
def run_analyze_tool(self, trial):
if self.prefix and not trial.stem.startswith(self.prefix):
# skip file if user specified a prefix and prefix is not present in current file
pass
else:
print(f'\t{trial.stem}')
# model
model = osim.Model(self.model_input)
model.initSystem()
# get starting and ending time
motion = osim.Storage(f'{trial.resolve()}')
first_time = motion.getFirstTime()
last_time = motion.getLastTime()
# prepare external forces xml file
if self.xml_forces:
external_loads = osim.ExternalLoads(model, self.xml_forces)
if self.prefix:
external_loads.setDataFileName(
f"{Path(self.ext_forces_dir, trial.stem.replace(f'{self.prefix}_', '')).resolve()}.sto"
)
else:
external_loads.setDataFileName(
f"{Path(self.ext_forces_dir, trial.stem).resolve()}.sto"
)
external_loads.setExternalLoadsModelKinematicsFileName(f'{trial.resolve()}')
if self.low_pass:
external_loads.setLowpassCutoffFrequencyForLoadKinematics(self.low_pass)
temp_xml = Path(f'{trial.stem}_temp.xml')
external_loads.printToXML(f'{temp_xml.resolve()}') # temporary xml file
current_class = self.get_class_name()
params = self.parse_analyze_set_xml(self.xml_input, node=current_class)
if current_class == 'StaticOptimization':
analysis = osim.StaticOptimization(model)
analysis.setUseModelForceSet(params['use_model_force_set'])
analysis.setActivationExponent(params['activation_exponent'])
analysis.setUseMusclePhysiology(params['use_muscle_physiology'])
analysis.setConvergenceCriterion(params['optimizer_convergence_criterion'])
analysis.setMaxIterations(int(params['optimizer_max_iterations']))
elif current_class == 'MuscleAnalysis':
analysis = osim.MuscleAnalysis(model)
analysis.setComputeMoments(params['compute_moments'])
elif current_class == 'JointReaction':
# construct joint reaction analysis
analysis = osim.JointReaction(model)
# analysis.setForcesFileName(
# f"{Path(self.muscle_forces_dir, trial.stem).resolve()}_StaticOptimization_force.sto"
# )
joint = osim.ArrayStr()
joint.append(params['joint_names'].replace(' ', ''))
analysis.setJointNames(joint)
body = osim.ArrayStr()
body.append(params['apply_on_bodies'].replace(' ', ''))
analysis.setOnBody(body)
frame = osim.ArrayStr()
frame.append(params['express_in_frame'].replace(' ', ''))
analysis.setInFrame(frame)
else:
raise ValueError('AnalyzeTool must be called from a child class')
analysis.setModel(model)
analysis.setName(current_class)
analysis.setOn(params['on'])
analysis.setStepInterval(int(params['step_interval']))
analysis.setInDegrees(params['in_degrees'])
analysis.setStartTime(first_time)
analysis.setEndTime(last_time)
model.addAnalysis(analysis)
# analysis tool
analyze_tool = osim.AnalyzeTool(model)
analyze_tool.setName(trial.stem)
analyze_tool.setModel(model)
analyze_tool.setModelFilename(Path(self.model_input).stem)
if self.xml_actuators:
force_set = osim.ArrayStr()
force_set.append(self.xml_actuators)
analyze_tool.setForceSetFiles(force_set)
analyze_tool.updateModelForces(model, self.xml_actuators)
analyze_tool.setInitialTime(first_time)
analyze_tool.setFinalTime(last_time)
if self.low_pass:
analyze_tool.setLowpassCutoffFrequency(self.low_pass)
analyze_tool.setCoordinatesFileName(f'{trial.resolve()}')
analyze_tool.setExternalLoadsFileName(f'{temp_xml}')
analyze_tool.setLoadModelAndInput(True)
analyze_tool.setResultsDir(f'{self.sto_output}')
analyze_tool.run()
if self.xml_forces:
temp_xml.unlink() # delete temporary xml file
if self.remove_empty_files:
self._remove_empty_files(directory=self.sto_output)
#Set output filename
idTool[ii-startInd][tt].setOutputGenForceFileName(dynamicFiles[tt].split('.')[0]+'_id.sto')
#Print and run tool
idTool[ii-startInd][tt].printToXML(dynamicFiles[tt].split('.')[0]+'_setupID.xml')
idTool[ii-startInd][tt].run()
##### NOTE: filter ID results given lack of CoP noise
#Print confirmation
print('ID complete for '+dynamicFiles[tt].split('.')[0])
#Run analysis to extract body kinematics
#Initialise analysis tool
anTool[ii-startInd].append(osim.AnalyzeTool())
#Set the model
anTool[ii-startInd][tt].setModelFilename(subList[ii]+'_scaledModelAdjusted_sensors.osim')
#Set times
anTool[ii-startInd][tt].setStartTime(startTime)
anTool[ii-startInd][tt].setFinalTime(endTime)
#Set external loads file
anTool[ii-startInd][tt].setExternalLoadsFileName(dynamicFiles[tt].split('.')[0]+'_grf'+'.xml')
#Set kinematics
anTool[ii-startInd][tt].setCoordinatesFileName(dynamicFiles[tt].split('.')[0]+'_ik.mot')
#Set lowpass filter frequency for kinematics (10Hz)
def perform_jra(model_file, ik_file, grf_file, grf_xml, reserve_actuators,
muscle_forces_file, results_dir, prefix, joint_names,
apply_on_bodies, express_in_frame):
"""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
muscle_forces_file: str
path to the file containing the muscle forces from SO
results_dir: str
directory to store the results
prefix: str
prefix of the resultant joint reaction loads
joint_names: list
joint names of interest
apply_on_bodies: list
apply on child or parent
express_in_frame: list
frame to express results
"""
assert (len(joint_names) == len(apply_on_bodies) == len(express_in_frame))
# 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')
# construct joint reaction analysis
motion = opensim.Storage(ik_file)
joint_reaction = opensim.JointReaction(model)
joint_reaction.setName('JointReaction')
joint_reaction.setStartTime(motion.getFirstTime())
joint_reaction.setEndTime(motion.getLastTime())
joint_reaction.setForcesFileName(muscle_forces_file)
joint_names_arr = opensim.ArrayStr()
apply_on_bodies_arr = opensim.ArrayStr()
express_in_frame_arr = opensim.ArrayStr()
for j, b, f in zip(joint_names, apply_on_bodies, express_in_frame):
joint_names_arr.append(j)
print(j)
apply_on_bodies_arr.append(b)
express_in_frame_arr.append(f)
joint_reaction.setJointNames(joint_names_arr)
joint_reaction.setOnBody(apply_on_bodies_arr)
joint_reaction.setInFrame(express_in_frame_arr)
model.addAnalysis(joint_reaction)
model.initSystem()
# analysis
analysis = opensim.AnalyzeTool(model)
analysis.setName(prefix + name)
analysis.setModel(model)
analysis.setModelFilename(model_file)
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()
jra_file = results_dir + name + '_JointReaction_ReactionLoads.sto'
return jra_file
model.getForceSet().append(pelvis_Mz_torque_actuator)
# Add point actuators
pelvis_Fx_point_actuator = createPointActuator('pelvis', (-0.034, 0.0, 0),
(1, 0, 0), 'pelvis_FX')
pelvis_Fy_point_actuator = createPointActuator('pelvis', (-0.034, 0.0, 0),
(0, 1, 0), 'pelvis_Fy')
pelvis_Fz_point_actuator = createPointActuator('pelvis', (-0.034, 0.0, 0),
(0, 0, 1), 'pelvis_Fz')
model.getForceSet().append(pelvis_Fx_point_actuator)
model.getForceSet().append(pelvis_Fy_point_actuator)
model.getForceSet().append(pelvis_Fz_point_actuator)
#Analyze / SO tool
analyze_tool = opensim.AnalyzeTool(
os.path.join(location_XMLs, so_analyze_file), False)
analyze_tool.setModel(model)
# analyzeTool.setModelFilename(osimModel.getDocumentFileName());
analyze_tool.setInitialTime(so_start_time)
analyze_tool.setFinalTime(so_end_time)
analyze_tool.setLowpassCutoffFrequency(kinematic_filter_frequency)
analyze_tool.setCoordinatesFileName(
os.path.join(location_motion_data, save_ik_name))
analyze_tool.setExternalLoadsFileName(
os.path.join(location_motion_data, save_external_loads_name))
analyze_tool.setLoadModelAndInput(True)
analyze_tool.setResultsDir(location_motion_data)
# These are parameters that can be used to programatically alter the optimization parameters
# analyze_tool.setReplaceForceSet(False)
# analyze_tool.setOutputPrecision(6)
