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_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 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 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)
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(
"analyze_MuscleAnalysis_FiberVelocity.sto")
time = table_force.getIndependentColumn()
force = table_force.getDependentColumn("muscle").to_numpy()
velocity = table_velocity.getDependentColumn("muscle").to_numpy()
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_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)
