def perform_id(events_file, model_file, ik_file, grf_file, grf_xml_file,
results_dir, opensimtools_dir, opensimplugin_dir, settings_dir):
"""Performs Inverse dynamics using Opensim."""
# model
model = opensim.Model(model_file)
trial = os.path.basename(grf_file).strip('_GRF.mot')
# external_loads = opensim.ExternalLoads(model, grf_xml_file)
# external_loads.setExternalLoadsModelKinematicsFileName(ik_file)
# external_loads.setDataFileName(grf_file)
# external_loads.setLowpassCutoffFrequencyForLoadKinematics(6)
# external_loads.printToXML(settings_dir + name + 'ExternalLoads.xml')
# create the setuo file
model.initSystem()
id_tool = opensim.InverseDynamicsTool()
id_tool.setName(trial)
id_tool.setModel(model)
id_tool.setExternalLoadsFileName(grf_xml_file)
id_tool.setResultsDir(results_dir)
id_tool.setStartTime(events_file.InitialContactTime.iloc[0])
id_tool.setEndTime(events_file.TimeLowestCOMX.iloc[1])
id_tool.setCoordinatesFileName(ik_file)
id_tool.setOutputGenForceFileName(trial + '_ID.sto')
id_tool.setLowpassCutoffFrequency(6)
id_xml = settings_dir + trial + '_Setup_ID.xml'
id_tool.printToXML(id_xml)
id_tool.run()
id_file = results_dir + trial + '_ID.sto'
return id_file
def run_id_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}')
# initialize inverse dynamic tool from setup file
model = osim.Model(self.model_input)
id_tool = osim.InverseDynamicsTool(self.xml_input)
id_tool.setModel(model)
# get starting and ending time
motion = osim.Storage(f'{trial.resolve()}')
start = motion.getFirstTime()
end = motion.getLastTime()
# inverse dynamics tool
id_tool.setStartTime(start)
id_tool.setEndTime(end)
id_tool.setCoordinatesFileName(f'{trial.resolve()}')
if self.low_pass:
id_tool.setLowpassCutoffFrequency(self.low_pass)
# set name of input (mot) file and output (sto)
filename = f'{trial.stem}'
id_tool.setName(filename)
id_tool.setOutputGenForceFileName('inverse_dynamic_output.sto')
id_tool.setResultsDir(f'{self.sto_output}')
# external loads file
if self.forces_dir:
loads = osim.ExternalLoads(self.xml_forces, True)
if self.prefix:
loads.setDataFileName(
f"{Path(self.forces_dir, trial.stem.replace(f'{self.prefix}_', '')).resolve()}.sto"
)
else:
loads.setDataFileName(
f"{Path(self.forces_dir, trial.stem).resolve()}.sto")
loads.setExternalLoadsModelKinematicsFileName(
f'{trial.resolve()}')
temp_xml = Path(f'{trial.stem}_temp.xml')
loads.printToXML(f'{temp_xml.resolve()}') # temporary xml file
id_tool.setExternalLoadsFileName(f'{temp_xml}')
else:
id_tool.setExternalLoadsFileName(self.xml_forces)
id_tool.printToXML(self.xml_output)
id_tool.run()
if self.forces_dir:
temp_xml.unlink() # delete temporary xml file
def setup_ID_xml(trial: str, model: str, directory: str, time_range: list,
cut_off_freq: np.float64):
'''
Rewrites the ID setup xml file for a new trial
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
'''
# Create an instance of the inverse dynamics tool
ID_tool = osim.InverseDynamicsTool()
# Set tool name
ID_tool.setName(model)
# Set the opensim model name
ID_tool.setModelFileName(directory + "\\" + model + "\\" + model + ".osim")
# Set excluded forces
excluded_forces = osim.ArrayStr()
excluded_forces.setitem(0, 'Muscles')
ID_tool.setExcludedForces(excluded_forces)
# Set low pass cut-off frequency, NOTE: Must be a double (np.float64)
ID_tool.setLowpassCutoffFrequency(np.float64(cut_off_freq))
# Set the input and results directory
ID_tool.setResultsDir(directory + "\\" + model + "\\" + trial)
ID_tool.setInputsDir(directory + "\\" + model + "\\" + trial)
# Set the time range, NOTE: Must be a double (np.float64)
ID_tool.setStartTime(np.float64(time_range[0]))
ID_tool.setEndTime(np.float64(time_range[-1]))
# Set the external loads file
external_loads_file = directory + "\\" + model + "\\" + trial + "\\" + trial + 'ExternalLoads.xml'
ID_tool.setExternalLoadsFileName(external_loads_file)
# Set the coordinates file
coordindate_file = directory + "\\" + model + "\\" + trial + "\\" + trial + 'IKResults.mot'
ID_tool.setCoordinatesFileName(coordindate_file)
# Set the output file
output_file_name = trial + "IDResults.sto"
ID_tool.setOutputGenForceFileName(output_file_name)
''' Write changes to an XML setup file '''
xml_setup_path = directory + "\\" + model + "\\" + trial + "\\" + trial + "IDSetup.xml"
ID_tool.printToXML(xml_setup_path)
def calc_net_generalized_forces(model, motion):
model.initSystem()
net_joint_moments = None
import tempfile
with tempfile.TemporaryDirectory() as tmpdirname:
id_tool = osim.InverseDynamicsTool()
modelID = osim.Model(model)
id_tool.setModel(modelID)
if type(motion) == osim.Storage:
id_tool.setLowpassCutoffFrequency(6)
storage = motion
else:
table = motion.exportToStatesTable()
labels = list(table.getColumnLabels())
import re
for ilabel in range(len(labels)):
labels[ilabel] = labels[ilabel].replace('/value', '')
labels[ilabel] = re.sub('/jointset/(.*?)/', '', labels[ilabel])
table.setColumnLabels(labels)
storage = osim.convertTableToStorage(table)
# TODO: There's a bug in converting column labels in
# convertTableToStorage().
stolabels = osim.ArrayStr()
stolabels.append('time')
for label in labels:
stolabels.append(label)
storage.setColumnLabels(stolabels)
id_tool.setCoordinateValues(storage)
# id_tool.setExternalLoadsFileName(extloads_fpath)
excludedForces = osim.ArrayStr()
excludedForces.append('ACTUATORS')
id_tool.setExcludedForces(excludedForces)
id_result = 'joint_moment_breakdown_residuals.sto'
id_tool.setResultsDir(tmpdirname)
id_tool.setOutputGenForceFileName(id_result)
# TODO: Remove muscles from the model?
id_tool.run()
net_joint_moments = osim.TimeSeriesTable(
os.path.join(tmpdirname, id_result))
return net_joint_moments
PFF_MOT_file = PFF_MOT_files[0]
path, filename = os.path.split(MOT_file)
filename, ext = os.path.splitext(filename)
STO_file = filename + '.sto' # Path to the output .MOT file that will be created and contain the IK results
XML_ID_file = dir_path + 'XML\\' + filename + '_ID.xml' # Path to the ID XML file that will be created
XML_External_Load_ID_file = dir_path + 'XML\\' + filename + '_External_Load_ID.xml' # Path to the External Load ID XML file that will be created
# Mot Data
motData = osim.Storage(MOT_file)
initial_time = motData.getFirstTime()
final_time = motData.getLastTime()
# ID tool
idTool = osim.InverseDynamicsTool(XML_generic_ID_path)
idTool.setResultsDir(dir_path + '\\STO\\')
idTool.setName(filename)
idTool.setModel(osimModel)
idTool.setCoordinatesFileName(MOT_file)
idTool.setStartTime(initial_time)
idTool.setEndTime(final_time)
idTool.setOutputGenForceFileName(STO_file)
# External Load File
externalLoads = osim.ExternalLoads(osimModel,
XML_generic_External_Load_ID_path)
externalLoads.setName(filename)
externalLoads.setDataFileName(PFF_MOT_file) # Set the PFF MOT filename
externalLoads.setLowpassCutoffFrequencyForLoadKinematics(4)
def plot_passive_joint_moments(model, coord_table,
coord_paths, muscle_paths=None):
model.initSystem()
# for muscle in model.getMuscleList():
# muscle.set_ignore_tendon_compliance(True)
# model.initSystem()
num_coords = len(coord_paths)
if not muscle_paths:
muscle_paths = list()
for muscle in model.getMuscleList():
muscle_paths.append(muscle.getAbsolutePathString())
num_muscles = len(muscle_paths)
labels = list(coord_table.getColumnLabels())
import re
for ilabel in range(len(labels)):
labels[ilabel] = labels[ilabel].replace('/value', '')
labels[ilabel] = re.sub('/jointset/(.*?)/', '', labels[ilabel])
coord_table.setColumnLabels(labels)
storage = osim.convertTableToStorage(coord_table)
# TODO: There's a bug in converting column labels in
# convertTableToStorage().
stolabels = osim.ArrayStr()
stolabels.append('time')
for label in labels:
stolabels.append(label)
storage.setColumnLabels(stolabels)
net_joint_moments = None
import tempfile
with tempfile.TemporaryDirectory() as tmpdirname:
id_tool = osim.InverseDynamicsTool()
modelID = osim.Model(model)
id_tool.setModel(modelID)
id_tool.setCoordinateValues(storage)
id_tool.setLowpassCutoffFrequency(6)
# id_tool.setExternalLoadsFileName(extloads_fpath)
excludedForces = osim.ArrayStr()
excludedForces.append('ACTUATORS')
id_tool.setExcludedForces(excludedForces)
id_result = 'joint_moment_breakdown_residuals.sto'
id_tool.setResultsDir(tmpdirname)
id_tool.setOutputGenForceFileName(id_result)
# TODO: Remove muscles from the model?
id_tool.run()
net_joint_moments = osim.TimeSeriesTable(
os.path.join(tmpdirname, id_result))
time = coord_table.getIndependentColumn()
states_traj = osim.StatesTrajectory.createFromStatesStorage(model, storage,
True, True,
True)
# TODO for models without activation dynamics, we must prescribeControlsToModel().
fig = pl.figure(figsize=(8.5, 11))
tendon_forces = np.empty((len(time), num_muscles))
for imusc, muscle_path in enumerate(muscle_paths):
muscle = model.getComponent(muscle_path)
for itime in range(len(time)):
state = states_traj.get(itime)
state.updU().setToZero()
muscle.setActivation(state, 0.01)
model.realizeVelocity(state)
muscle.computeEquilibrium(state)
model.realizeDynamics(state)
tendon_forces[itime, imusc] = muscle.getTendonForce(state)
for icoord, coord_path in enumerate(coord_paths):
coord = model.getComponent(coord_path)
label = os.path.split(coord_path)[-1] + '_moment'
net_moment = toarray(net_joint_moments.getDependentColumn(label))
moment_arms = np.empty((len(time), num_muscles))
for imusc, muscle_path in enumerate(muscle_paths):
muscle = model.getComponent(muscle_path)
for itime in range(len(time)):
state = states_traj.get(itime)
moment_arms[itime, imusc] = \
muscle.computeMomentArm(state, coord)
ax = fig.add_subplot(num_coords, 1, icoord + 1)
# net_integ = np.trapz(np.abs(net_moment), x=time)
sum_actuators_shown = np.zeros_like(time)
for imusc, muscle_path in enumerate(muscle_paths):
if np.any(moment_arms[:, imusc]) > 0.00001:
this_moment = tendon_forces[:, imusc] * moment_arms[:, imusc]
mom_integ = np.trapz(np.abs(this_moment), time)
if mom_integ > 0.5:
ax.plot(time, this_moment, label=muscle_path)
sum_actuators_shown += this_moment
ax.plot(time, sum_actuators_shown,
label='sum actuators shown', color='gray', linewidth=2)
time_net = np.array(net_joint_moments.getIndependentColumn())
filter = (time_net > time[0]) & (time_net < time[-1])
# ax.plot(time_net[filter], net_moment[filter],
# label='net', color='black', linewidth=2)
ax.set_title(coord_path)
ax.set_ylabel('moment (N-m)')
ax.legend(frameon=False, bbox_to_anchor=(1, 1),
loc='upper left', ncol=2)
ax.tick_params(axis='both')
ax.set_xlim([time[0], time[-1]])
ax.set_xlabel('time (% gait cycle)')
fig.tight_layout()
return fig
# #Set output filename
# ikTool[ii-startInd][tt].set_output_motion_file(dynamicFiles[tt].split('.')[0]+'_ik.mot')
# #Print and run tool
# ikTool[ii-startInd][tt].printToXML(dynamicFiles[tt].split('.')[0]+'_setupIK.xml')
# ikTool[ii-startInd][tt].run()
# #Rename marker errors file
# shutil.move('_ik_marker_errors.sto',dynamicFiles[tt].split('.')[0]+'_ik_marker_errors.sto')
# #Print confirmation
# print('IK complete for '+dynamicFiles[tt].split('.')[0])
#Initialise ID tool
idTool[ii-startInd].append(osim.InverseDynamicsTool())
#Set the model
idTool[ii-startInd][tt].setModelFileName(subList[ii]+'_scaledModelAdjusted_sensors.osim')
#Set times
idTool[ii-startInd][tt].setStartTime(startTime)
idTool[ii-startInd][tt].setEndTime(endTime)
#Set external loads file
idTool[ii-startInd][tt].setExternalLoadsFileName(dynamicFiles[tt].split('.')[0]+'_grf'+'.xml')
#Set kinematics
idTool[ii-startInd][tt].setCoordinatesFileName(dynamicFiles[tt].split('.')[0]+'_ik.mot')
#Set lowpass filter frequency for kinematics (10Hz)
def inverseDynamics():
import os
import re
import shutil
import opensim as osim
import directories
allDir = list(directories.main(directories))
parentDir = allDir[0]
paramsDir = allDir[1]
subID = allDir[4]
subResultsDir = allDir[5]
ikResultsDir = allDir[6]
idResultsDir = allDir[7]
# Clear Inverse Dynamics Folder
if os.path.exists(idResultsDir):
shutil.rmtree(idResultsDir, ignore_errors=True)
if not os.path.exists(idResultsDir):
os.mkdir(idResultsDir)
# Input data files
genericExtLoads = paramsDir + "/externalLoads.xml"
motData = parentDir + "/data/osDemo/subject01_walk1_grf.mot"
motFileName = "subject01_walk1_grf.mot"
# saveDir = subResultsDir + "/" + subID + "motionFile.mot"
ikFileName = "subject01_walk1_ik.mot"
ikFile = ikResultsDir + "/" + ikFileName
# Copy GRF File over to Current Directory
shutil.copy(motData, idResultsDir + "/" + motFileName)
# Load Inverse Kinematics Model
aModel = osim.Model(subResultsDir + "/" + subID + ".osim")
# initialize system
aModel.initSystem()
# Initialize External Loads File from Generic File
extLoads = osim.ExternalLoads(aModel, genericExtLoads)
# Initialize idTool
idTool = osim.InverseDynamicsTool()
idTool.setLowpassCutoffFrequency(6.0)
idTool.setInputsDir(idResultsDir)
idTool.setResultsDir(idResultsDir)
idTool.setModel(aModel)
idTool.setModelFileName(subResultsDir + "/" + subID + ".osim")
# Get .mot data to determine time range
motCoordsData = osim.Storage(ikFile)
# Get initial and final time
initial_time = motCoordsData.getFirstTime()
final_time = motCoordsData.getLastTime()
# Creat output ID
idFileName = re.sub('ik.mot', 'id.sto', ikFileName)
# Customize and save external loads ile
extLoads.setName(motFileName)
extLoads.setDataFileName(motData)
extLoads.setExternalLoadsModelKinematicsFileName(ikFile)
extLoads.printToXML(idResultsDir + "/" +
re.sub('ik.mot', 'extLoads.xml', ikFileName))
# Setup idTool
idTool.setName(motFileName)
idTool.setCoordinatesFileName(ikFile)
idTool.setStartTime(initial_time)
idTool.setEndTime(final_time)
# Must be relative to output directory, not full path!
idTool.setOutputGenForceFileName(idFileName)
idTool.setExternalLoadsFileName(
idResultsDir + "/" + re.sub('ik.mot', 'extLoads.xml', ikFileName))
# Can comment out if not needed in GUI
idTool.printToXML(idResultsDir + "/" +
re.sub('ik.mot', 'setupID.xml', ikFileName))
# Run idTool
idTool.run()
os.system('cls' if os.name == 'nt' else 'clear')
return ()
os.path.join(location_motion_data, save_ik_name))
ik_tool.run()
#Build external loads file and save to disk - this will be loaded in for IK and SO
external_loads = opensim.ExternalLoads(
os.path.join(location_XMLs, external_loads_xml), True)
external_loads.setLowpassCutoffFrequencyForLoadKinematics(
kinematic_filter_frequency)
external_loads.setDataFileName(
os.path.join(location_motion_data, pedal_data_filenames))
external_loads.setName('both_pedal_forces')
external_loads.printToXML(
os.path.join(location_motion_data, save_external_loads_name))
#perform ID
id_tool = opensim.InverseDynamicsTool()
id_tool.setModel(model)
# id_tool.setModelFileName()
id_tool.setCoordinatesFileName(os.path.join(location_motion_data,
save_ik_name))
id_tool.setLowpassCutoffFrequency(kinematic_filter_frequency)
id_tool.setResultsDir(location_motion_data)
id_tool.setOutputGenForceFileName(save_id_name)
id_tool.setStartTime(id_start_time)
id_tool.setEndTime(id_end_time)
excludedForces = opensim.ArrayStr()
excludedForces.append('Muscles')
id_tool.setExcludedForces(excludedForces)
id_tool.setExternalLoadsFileName(
os.path.join(location_motion_data, save_external_loads_name))
