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AFO10_OpenSimAPI.py
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AFO10_OpenSimAPI.py
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import os
import opensim
import numpy as np
def LigMechanicsMax (Sim_output_folder, Sim_results, osimModel):
# Aims: to export the maximum lengths and forces of the ligaments (i.e. AFO straps) during a specific motion
# Inputs: osimModel: the opensim model with ligaments
# motSto_file: the motion file loaded to the model for length and forces exportion
# The folder path of pthon script
path_script = os.path.realpath(__file__) # The full path for the python scrip folder: Simulation_printAFO
path_simulation=os.path.dirname(os.path.dirname(path_script)) # The path of the folder including the python script:Simulation_printAFO_CAMG
# Set and update the path to the local OpenSim geometry directory
path='C:\OpenSim 4.1\Geometry'
opensim.ModelVisualizer.addDirToGeometrySearchPaths(path)
# Load the MSK model
osimModel=os.path.join(path_simulation, osimModel)
myModel=opensim.Model(osimModel) # Load the opensim model
state=myModel.initSystem() # Initial state
# Load the motion file
motSto_file=os.path.join(path_simulation, Sim_output_folder, Sim_results)
motSto_file_type='states' in motSto_file # Determine whether the file name includes 'states' or not, will be used in the below syntax
# Storage the simulation results of motion
motSto=opensim.Storage(motSto_file)
timestep_motSto=motSto.getSize() # The number of time step
coords=myModel.getCoordinateSet()
num_coords=coords.getSize() # Get the number of coordinates in the model, including coordinates of forceset, such as BackBushing et al.
# Update each model coordinate for each time frame
vars=['ankle_angle_r', 'subtalar_angle_r'] # The coordinates that will be updated for calculate the ligament length
motSto_num=timestep_motSto # The number of time instances selected for ligament lengths and forces
motSto_interval=int(timestep_motSto/motSto_num) # The number of intervals for the time instances
strap_lengths=[]
strap_forces=[]
for j in range (0,motSto_num):
for i, var in enumerate (vars):
coordvalue=opensim.ArrayDouble()
#currentcoord=coords.get(i).getName() # Get the name of coordinates in opensim model
if motSto_file_type==True:
currentcoord_fullname='/jointset/'+var.replace('_angle_', '_')+'/'+var+'/value'
else:
currentcoord_fullname=var
motSto.getDataColumn(currentcoord_fullname, coordvalue)
q=coordvalue.getitem(j*motSto_interval)
myModel.updCoordinateSet().get(var).setValue(state, np.radians(q), False)
myModel.assemble(state)
myModel.realizePosition(state)
# Access ligament in models forceset & get ligament length after safedoncast
fset=myModel.getForceSet()
strap1=opensim.Ligament.safeDownCast(fset.get("orthosis_1"))
strap2=opensim.Ligament.safeDownCast(fset.get("orthosis_2"))
#strap3=opensim.Ligament.safeDownCast(fset.get("orthosis_3"))
#strap4=opensim.Ligament.safeDownCast(fset.get("orthosis_4"))
# strap_lengths.append([strap1.getLength(state), strap2.getLength(state), strap3.getLength(state), strap4.getLength(state)])
strap_lengths.append([strap1.getLength(state), strap2.getLength(state)])
myModel.computeStateVariableDerivatives(state)
# strap_forces.append([strap1.getTension(state), strap2.getTension(state), strap3.getTension(state), strap4.getTension(state)])
strap_forces.append([strap1.getTension(state), strap2.getTension(state)])
strap_lengths_realtime=np.array(strap_lengths).T
strap_forces_realtime=np.array(strap_forces).T
strap_lengths_max=np.max(np.array(strap_lengths).T, axis=1)
strap_forces_max=np.max(np.array(strap_forces).T, axis=1)
return strap_lengths_realtime, strap_forces_realtime, strap_lengths_max, strap_forces_max
#
def LigSetRestingLength(osimModel):
# Set the resting length for the ligament (strap)
# Set and update the path to the local OpenSim geometry directory
path='C:\OpenSim 4.1\Geometry'
opensim.ModelVisualizer.addDirToGeometrySearchPaths(path)
# Load the model
myModel=opensim.Model(osimModel) # Load the opensim model
state=myModel.initSystem() # Initial state
fset=myModel.getForceSet()
strap1=opensim.Ligament.safeDownCast(fset.get("orthosis_1"))
strap2=opensim.Ligament.safeDownCast(fset.get("orthosis_2"))
# strap3=opensim.Ligament.safeDownCast(fset.get("orthosis_3"))
# strap4=opensim.Ligament.safeDownCast(fset.get("orthosis_4"))
# Get the lengths of the straps in the MSK model
strap1_length=strap1.getLength(state)
strap2_length=strap2.getLength(state)
# strap3_length=strap3.getLength(state)
# strap4_length=strap4.getLength(state)
# Set the resting lengths for the straps using the extracted lengths
strap1.set_resting_length(strap1_length)
strap2.set_resting_length(strap2_length)
# strap3.set_resting_length(strap3_length)
# strap4.set_resting_length(strap4_length)
myModel.printToXML(osimModel)
#
def Liginitstates(osimModel): # Define the raltive path of opensim model, e.g. relative to the python code
# Aims: to export the lengths and forces of the ligaments (i.e. AFO straps) at the initial state of model
# Inputs: osimModel: the opensim model with ligaments
# Set and update the path to the local OpenSim geometry directory
# Set and update the path to the local OpenSim geometry directory
# The folder path of pthon script
path_script = os.path.realpath(__file__) # The full path for the python scrip folder: Simulation_printAFO
path_simulation=os.path.dirname(os.path.dirname(path_script)) # The path of the folder including the python script:Simulation_printAFO_CAMG
# Set and update the path to the local OpenSim geometry directory
path='C:\OpenSim 4.1\Geometry'
opensim.ModelVisualizer.addDirToGeometrySearchPaths(path)
# Load the MSK model
osimModel=os.path.join(path_simulation, osimModel)
# Load the model
myModel=opensim.Model(osimModel) # Load the opensim model
state=myModel.initSystem() # Initial state
fset=myModel.getForceSet()
strap1=opensim.Ligament.safeDownCast(fset.get("orthosis_1"))
strap2=opensim.Ligament.safeDownCast(fset.get("orthosis_2"))
# strap3=opensim.Ligament.safeDownCast(fset.get("orthosis_3"))
# strap4=opensim.Ligament.safeDownCast(fset.get("orthosis_4"))
# strap_lengths=[strap1.getLength(state), strap2.getLength(state), strap3.getLength(state), strap4.getLength(state)]
strap_lengths=[strap1.getLength(state), strap2.getLength(state)]
myModel.computeStateVariableDerivatives(state)
# strap_forces=[strap1.getTension(state), strap2.getTension(state), strap3.getTension(state), strap4.getTension(state)]
strap_forces=[strap1.getTension(state), strap2.getTension(state)]
return strap_lengths, strap_forces
#
def LigMechanicsRealtime (osimModel, motSto_file):
# Aims: to export the real time lengths and forces of the ligaments (i.e. AFO straps) during a specific motion
# Inputs: osimModel: the opensim model with ligaments
# motSto_file: the motion file loaded to the model for length and forces exportion
# Set and update the path to the local OpenSim geometry directory
path='C:\OpenSim 4.1\Geometry'
opensim.ModelVisualizer.addDirToGeometrySearchPaths(path)
# Load the model
#osimModel='D:\Drop landing\Fullbodymodel_droplanding_AFO.osim' # File path for opensim model
#motSto_file='D:\Drop landing\DL simulation results\\11.mot' # File path for motion file
myModel=opensim.Model(osimModel) # Load the opensim model
state=myModel.initSystem() # Initial state
motSto_file_type='states' in motSto_file # Determine whether the file name includes 'states' or not, will be used in the below syntax
# Storage the simulation results of motion
motSto=opensim.Storage(motSto_file)
timestep_motSto=motSto.getSize() # The number of time step
coords=myModel.getCoordinateSet()
num_coords=coords.getSize() # Get the number of coordinates in the model, including coordinates of forceset, such as BackBushing et al.
# Update each model coordinate for each time frame
vars=['ankle_angle_r', 'subtalar_angle_r'] # The coordinates that will be updated for calculate the ligament length
motSto_num=timestep_motSto # The number of time instances selected for ligament lengths and forces
motSto_interval=int(timestep_motSto/motSto_num) # The number of intervals for the time instances
strap_lengths=[]
strap_forces=[]
for j in range (1,motSto_num):
for i, var in enumerate (vars):
coordvalue=opensim.ArrayDouble()
#currentcoord=coords.get(i).getName() # Get the name of coordinates in opensim model
if motSto_file_type==True:
currentcoord_fullname='/jointset/'+var.replace('_angle_', '_')+'/'+var+'/value'
else:
currentcoord_fullname=var
motSto.getDataColumn(currentcoord_fullname, coordvalue)
q=coordvalue.getitem(j*motSto_interval)
myModel.updCoordinateSet().get(var).setValue(state, np.radians(q), False)
myModel.assemble(state)
myModel.realizePosition(state)
# Access ligament in models forceset & get ligament length after safedoncast
fset=myModel.getForceSet()
strap1=opensim.Ligament.safeDownCast(fset.get("orthosis_1"))
strap2=opensim.Ligament.safeDownCast(fset.get("orthosis_2"))
# strap3=opensim.Ligament.safeDownCast(fset.get("orthosis_3"))
# strap4=opensim.Ligament.safeDownCast(fset.get("orthosis_4"))
# strap_lengths.append([strap1.getLength(state), strap2.getLength(state), strap3.getLength(state), strap4.getLength(state)])
strap_lengths.append([strap1.getLength(state), strap2.getLength(state)])
myModel.computeStateVariableDerivatives(state)
# strap_forces.append([strap1.getTension(state), strap2.getTension(state), strap3.getTension(state), strap4.getTension(state)])
strap_forces.append([strap1.getTension(state), strap2.getTension(state)])
strap_lengths=np.array(strap_lengths).T
strap_forces=np.array(strap_forces).T
return strap_lengths, strap_forces
#
def LigPeneMonitor(strap_lengths_realtime, strap_length_ini, threshold):
strap_lengths_grad=[]
strap_pene_monitor=[]
for strap_num in range (len(strap_lengths_realtime)):
strap_lengths_grad_temp=[]
strap_pene_monitor_temp='No Penetration'
strap_length_index=0
for i,j in zip(strap_lengths_realtime[strap_num], strap_lengths_realtime[strap_num][1:]):
strap_length_index+=1
strap_lengths_grad_temp.append(j-i)
if abs(j-i)>threshold:
print(j-i)
if strap_lengths_realtime[strap_num][strap_length_index] - strap_length_ini[strap_num] > 0:
strap_pene_monitor_temp='Penetration stretch'
else:
strap_pene_monitor_temp='Penetration slack'
strap_lengths_grad.append(strap_lengths_grad_temp)
strap_pene_monitor.append(strap_pene_monitor_temp)
return strap_lengths_grad, strap_pene_monitor
#
if __name__ == '__main__':
import pandas as pd
import matplotlib.pyplot as plt
output_folder_DL_platform0='D:\Trial\Gait simulation0\Model outputs\\4_CMC\\0'
osimModel_platform0='D:\Trial\Gait simulation0\Model outputs\\3_RRA\Fullbodymodel_Walk_RRA_final_AFO.osim'
[strap_lengths, strap_forces, strap_lengths_max, strap_forces_max]=LigMechanicsMax(output_folder_DL_platform0, 'cmc_Kinematics_q.sto', osimModel_platform0)
#[strap_length_grad, strap_pene_monitor]=LigPeneMonitor(strap_lengths, 0.004)
[strap_length_ini, strap_forces_ini]=Liginitstates(osimModel_platform0)
#strap_length_ini_reshape=np.array(strap_length_ini).reshape(-1,1)
#strap_length_rate=strap_lengths/strap_length_ini_reshape
[strap_length_grad, strap_pene_monitor]=LigPeneMonitor(strap_lengths, strap_length_ini, 0.004)
strap_length_grad_grad=[]
a=1
for num in range(len(strap_length_grad)):
strap_length_grad_grad_temp=[]
for i,j in zip (strap_length_grad[num], strap_length_grad[num][1:]):
strap_length_grad_grad_temp.append(j/i)
strap_length_grad_grad.append(strap_length_grad_grad_temp)
strap_length_grad=strap_length_grad_grad
#strap_length_grad=strap_lengths
[nrow,ncolumn]=np.array(strap_length_grad).shape
strap_length_grad_index=list(range(ncolumn))
print(strap_pene_monitor)
"""
osimModel='D:\Trial\Drop landing0\Fullbodymodel_DL_platform0_AFO.osim'
Results_file='D:\Trial\Drop landing0\DL simulation results\\02500\default_states_degrees1.mot'
[strap_length_ini, strap_force_ini]=Liginitstates(osimModel)
[strap_lengths, strap_forces]=LigMechanicsRealtime(osimModel, Results_file)
#strap_length_ini_reshape=np.array(strap_length_ini).reshape(-1,1)
#strap_length_rate=strap_lengths/strap_length_ini_reshape
#[nrow, ncolumn]=strap_lengths.shape
#strap_length_index=list(range(ncolumn))
strap_length_grad=[]
for strap_num in range (len(strap_lengths)):
strap_length_grad_temp=[]
for i,j in zip(strap_lengths[strap_num], strap_lengths[strap_num][1:]):
strap_length_grad_temp.append(j-i)
strap_length_grad.append(strap_length_grad_temp)
[nrow,ncolumn]=np.array(strap_length_grad).shape
strap_length_grad_index=list(range(ncolumn))
"""
plt.figure()
plt.subplot(2,2,1)
#plt.plot(strap_length_index, strap_lengths[0], marker='o', label='Strap lengths for strap 1')
#plt.plot(strap_length_index, strap_length_rate[0], marker='o', label='Strap lengths for strap 1')
plt.plot(strap_length_grad_index, strap_length_grad[0], marker='o', label='Strap lengths for strap 1')
#plt.xlim((0,800))
#plt.ylim((-0.02, 0.002))
plt.subplot(2,2,2)
#plt.plot(strap_length_index, strap_lengths[1], marker='o', label='Strap lengths for strap 2')
#plt.plot(strap_length_index, strap_length_rate[1], marker='o', label='Strap lengths for strap 2')
plt.plot(strap_length_grad_index, strap_length_grad[1], marker='o', label='Strap lengths for strap 2')
#plt.xlim((0,800))
#plt.ylim((-0.02, 0.002))
plt.subplot(2,2,3)
#plt.plot(strap_length_index, strap_lengths[2], marker='o', label='Strap lengths for strap 3')
#plt.plot(strap_length_index, strap_length_rate[2], marker='o', label='Strap lengths for strap 3')
plt.plot(strap_length_grad_index, strap_length_grad[2], marker='o', label='Strap lengths for strap 3')
#plt.xlim((0,800))
#plt.ylim((-0.02, 0.002))
plt.subplot(2,2,4)
#plt.plot(strap_length_index, strap_lengths[3], marker='o', label='Strap lengths for strap 4')
#plt.plot(strap_length_index, strap_length_rate[3], marker='o', label='Strap lengths for strap 4')
plt.plot(strap_length_grad_index, strap_length_grad[3], marker='o', label='Strap lengths for strap 4')
#plt.xlim((0,800))
#plt.ylim((-0.02, 0.002))
plt.show()
"""
# The plot of the force-length relationship in one figure
plt.figure()
plt.plot(strap_lengths[0], strap_forces[0], marker='o', label='Strap FL for strap 1')
plt.plot(strap_lengths[1], strap_forces[1], marker='o', label='Strap FL for strap 2')
plt.plot(strap_lengths[2], strap_forces[2], marker='o', label='Strap FL for strap 3')
plt.plot(strap_lengths[3], strap_forces[3], marker='o', label='Strap FL for strap 4')
plt.show()
"""
"""
# Save results to an excel files
exe_file='D:\Trial\Strap forces and lengths.xlsx'
sheet_name='Sheet1'
strap_length_forces=np.vstack((strap_lengths, strap_forces)).T
data_pd=pd.DataFrame(strap_length_forces)
data_pd.columns=['strap_1_length', 'strap_2_length', 'strap_3_length', 'strap_4_length', 'strap_1_force', 'strap_2_force', 'strap_3_force', 'strap_4_force']
data_writer=pd.ExcelWriter(exe_file)
data_pd.to_excel(data_writer, sheet_name)
data_writer.save()
data_writer.close()
#
"""
"""
# The API of getting the length and force in GUI
myModel=getCurrentModel()
fset=myModel.getForceSet()
strap=modeling.Ligament.safeDownCast(fset.get("orthosis_4"))
state=myModel.initSystem()
length=strap.getLength(state)
myModel.computeStateVariableDerivatives(state)
strap_force=strap.getTension(state)
"""