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calcContactForces.py
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calcContactForces.py
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import os
os.add_dll_directory('C:/Users/jonstingel/opensim/opensim-core-4.5-2024-05-15-a1a2282/bin')
import opensim as osim
import numpy as np
import pdb
import time
import matplotlib.pyplot as plt
import scipy
# naturalcolor = '#fdb863'
ncolor = '#e66101'
ncolorlight = '#fee0b6'
ncolor1 = '#fff5eb'
ncolor2 = '#fee6ce'
ncolor3 = '#fdd0a2'
ncolor4 = '#fdae6b'
ncolor5 = '#fd8d3c'
ncolor6 = '#f16913'
ncolor7 = '#d94801'
ncolor8 = '#a63603'
ncolor9 = '#7f2704'
# exotendoncolor = '#f1a340'
ecolor = '#5e3c99'
ecolorlight = '#d8daeb'
# function from Nick Bianco - not used in script, but used as reference for moco
def calc_knee_reaction_force(self, root_dir, solution):
modelProcessor = osim.ModelProcessor()
model = modelProcessor.process()
jr = osim.analyzeSpatialVec(model, solution,
['.*walker_knee.*reaction_on_parent.*'])
jr = jr.flatten(['_mx', '_my', '_mz', '_fx', '_fy', '_fz'])
traj = np.empty(jr.getNumRows())
max = -np.inf
for itime in range(jr.getNumRows()):
for irxn in range(int(jr.getNumColumns() / 6)):
fx = jr.getDependentColumnAtIndex(6 * irxn + 3)[itime]
fy = jr.getDependentColumnAtIndex(6 * irxn + 4)[itime]
fz = jr.getDependentColumnAtIndex(6 * irxn + 5)[itime]
norm = np.sqrt(fx**2 + fy**2 + fz**2)
traj[itime] = norm
max = np.max([norm, max])
time = jr.getIndependentColumn()
avg = np.trapz(traj, x=time) / (time[-1] - time[0])
# fig = plt.figure()
# ax = fig.add_subplot(1, 1, 1)
# ax.plot(time, traj)
# plt.show()
g = np.abs(model.get_gravity()[1])
state = model.initSystem()
mass = model.getTotalMass(state)
weight = mass * g
return max / weight, avg / weight
# simple helper to get the model mass
def get_model_total_mass(wkdir, filename):
model = osim.Model(os.path.join(wkdir, filename))
modelmass = model.getTotalMass(model.initSystem())
grav = np.abs(model.get_gravity()[1])
return modelmass*grav
# function that actually runs the analysis to compute knee contact force, and
# transforms it to the tibia frame
def computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag):
# '''
# intersegmental forces - method 2
# try the analysis
jr_tool = osim.AnalyzeTool()
jr_tool.setName('jr_analysis_100con')
# jr_tool.setModelFilename(os.path.join(trialdir, 'post_simple_model_all_the_probes_muscletrack.osim'))
# I don't think this is going to work.
# jr_tool.setStatesStorage(statesStorage)
# jr_tool.setStatesFileName('testfibsolution.sto')
trimmingstates = osim.Storage('trimmingStates_' + tag + '.sto')
jr_tool.setStatesStorage(trimmingstates)
# jr_tool.setExternalLoadsFileName('grf_walk.xml')
# jr_tool.updControllerSet().cloneAndAppend(osim.PrescribedController(os.path.join(trialdir, 'muscletrack_controls_100con.sto')))
jr_tool.updControllerSet().cloneAndAppend(osim.PrescribedController(os.path.join(trialdir, 'trimmingControls_' + tag + '.sto')))
jra = osim.JointReaction()
jra.setName('jra_' + tag)
wherestr = osim.ArrayStr(); wherestr.append('child')
jra.setInFrame(wherestr)
jr_tool.updAnalysisSet().cloneAndAppend(jra)
jr_tool.setInitialTime(initTime)
jr_tool.setFinalTime(finalTime)
jr_tool.setResultsDir(trialdir)
# jr_tool.setModelFilename('jratestingmodel.osim')
trimmodel.addAnalysis(jra)
jr_tool.setModel(trimmodel)
## uncomment to rerun the analysis
jr_tool.printToXML(os.path.join(trialdir, 'jr_setup.xml'))
# time.sleep(0.5)
# jr_tool = osim.AnalyzeTool(os.path.join(trialdir, 'jr_setup.xml'))
jr_tool.run()
time.sleep(0.5)
# '''
# figure out how to do an intersegmental with proper value of forces showing up.
trimjra = osim.TimeSeriesTable('jr_analysis_100con_jra_' + tag + '_ReactionLoads.sto')
trimjralabels = trimjra.getColumnLabels()
tiby = trimjra.getDependentColumn('walker_knee_r_on_tibia_r_in_tibia_r_fy').to_numpy()
# pdb.set_trace()
# import matplotlib.pyplot as plt
# plt.figure()
# plt.plot(np.array(trimjra.getIndependentColumn()), tiby)
return tiby
# method for computing the individual muscle contributions to knee contact force
def getKneeContactributions(trialdir, musclesWanted_split, tag):
# os.chdir(trialdir)
# solution = osim.MocoTrajectory('muscle_statetrack_grfprescribe_solution_100con.sto')
# model = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# # attempting with just setting muscles to not apply force
# muscles = model.getMuscles()
# for m in range(muscles.getSize()):
# musc = muscles.get(m)
# muscname = musc.getName()
# if muscname not in musclesWanted_split:
# musc.setMaxIsometricForce(0.0)
# # else:
# # print(muscname)
# model.initSystem()
if musclesWanted_split == []: # this is the inter or intersegmental condition
statesStorage = osim.Storage('muscletrack_states_100con.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
elif 'all' in musclesWanted_split:
statesStorage = osim.Storage('muscletrack_states_100con.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con.sto')
# in this case, we want all the muscles in the model
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
# in this case we want all the controls, not getting rid of any muscles
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# model keeping all the muscles again for this one
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
###
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
elif 'reserve' in musclesWanted_split:
statesStorage = osim.Storage('muscletrack_states_100con.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'lumbar' not in con:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it (or reserves?)
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
# print(fo.getName())
if 'lumbar' not in fo.getName() and 'HOBL' not in fo.getName():
getrid = True
trimforces.remove(f-count)
count += 1
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
elif 'none' in musclesWanted_split:
statesStorage = osim.Storage('muscletrack_states_100con.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it (or reserves?)
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
if 'HOBL' not in fo.getName():
getrid = True
trimforces.remove(f-count)
count += 1
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
else:
statesStorage = osim.Storage('muscletrack_states_100con.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con.sto')
# musclesWanted_split = ['1'2'3'4']
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
# print(stat)
getrid = True
for want in musclesWanted_split:
if want in stat:
# want this one
# print('want this one')
# print(stat)
getrid = False
if getrid:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want to keep this one
# print(stat)
getrid = False
if getrid:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
# print(con)
if'lumbar' not in con:
getrid = True
for want in musclesWanted_split:
if want in con:
# want this
# print('want this one')
# print(con)
getrid = False
if getrid:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# get rid of muscles that we don't want
trimmuscles = trimmodel.getMuscles()
numMuscles = trimmuscles.getSize()
count = 0
for m in range(numMuscles):
musc = trimmuscles.get(m-count)
# print(musc.getName())
getrid = True
for mu in musclesWanted_split:
# print(mu)
if mu == musc.getName():
# print(musc.getName())
# print(mu)
getrid = False
if getrid:
trimmuscles.remove(musc)
count +=1
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
# print(fo.getName())
if 'lumbar' not in fo.getName() and 'HOBL' not in fo.getName():
getrid = True
for mu in musclesWanted_split:
if mu == fo.getName():
getrid = False
if getrid:
trimforces.remove(f-count)
count += 1
# model should only have muscles that we want now.
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
###
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
return jray
# method for computing the individual muscle contributions to knee contact force
def getKneeContactributions001(trialdir, musclesWanted_split, tag):
# os.chdir(trialdir)
# solution = osim.MocoTrajectory('muscle_statetrack_grfprescribe_solution_100con.sto')
# model = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# # attempting with just setting muscles to not apply force
# muscles = model.getMuscles()
# for m in range(muscles.getSize()):
# musc = muscles.get(m)
# muscname = musc.getName()
# if muscname not in musclesWanted_split:
# musc.setMaxIsometricForce(0.0)
# # else:
# # print(muscname)
# model.initSystem()
if musclesWanted_split == []:
statesStorage = osim.Storage('muscletrack_states_100con001_2.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con001_2.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con001_2.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
else:
statesStorage = osim.Storage('muscletrack_states_100con001_2.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con001_2.sto')
# musclesWanted_split = ['1'2'3'4']
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want this one
# print(stat)
getrid = False
if getrid:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want to keep this one
# print(stat)
getrid = False
if getrid:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con001_2.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con001_2.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
getrid = True
for want in musclesWanted_split:
if want in con:
# want this
# print(con)
getrid = False
if getrid:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# get rid of muscles that we don't want
trimmuscles = trimmodel.getMuscles()
numMuscles = trimmuscles.getSize()
count = 0
for m in range(numMuscles):
musc = trimmuscles.get(m-count)
# print(musc.getName())
getrid = True
for mu in musclesWanted_split:
# print(mu)
if mu == musc.getName():
# print(musc.getName())
# print(mu)
getrid = False
if getrid:
trimmuscles.remove(musc)
count +=1
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
# print(fo.getName())
if 'reserve' not in fo.getName() and 'lumbar' not in fo.getName():
getrid = True
for mu in musclesWanted_split:
if mu == fo.getName():
getrid = False
if getrid:
trimforces.remove(f-count)
count += 1
# model should only have muscles that we want now.
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
###
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
return jray
# method for computing the individual muscle contributions to knee contact force
def getKneeContactributions0001(trialdir, musclesWanted_split, tag):
# os.chdir(trialdir)
# solution = osim.MocoTrajectory('muscle_statetrack_grfprescribe_solution_100con.sto')
# model = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# # attempting with just setting muscles to not apply force
# muscles = model.getMuscles()
# for m in range(muscles.getSize()):
# musc = muscles.get(m)
# muscname = musc.getName()
# if muscname not in musclesWanted_split:
# musc.setMaxIsometricForce(0.0)
# # else:
# # print(muscname)
# model.initSystem()
if musclesWanted_split == []:
statesStorage = osim.Storage('muscletrack_states_100con0001_2.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con0001_2.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con0001_2.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
else:
statesStorage = osim.Storage('muscletrack_states_100con0001_2.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con0001_2.sto')
# musclesWanted_split = ['1'2'3'4']
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want this one
# print(stat)
getrid = False
if getrid:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want to keep this one
# print(stat)
getrid = False
if getrid:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con0001_2.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con0001_2.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
getrid = True
for want in musclesWanted_split:
if want in con:
# want this
# print(con)
getrid = False
if getrid:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# get rid of muscles that we don't want
trimmuscles = trimmodel.getMuscles()
numMuscles = trimmuscles.getSize()
count = 0
for m in range(numMuscles):
musc = trimmuscles.get(m-count)
# print(musc.getName())
getrid = True
for mu in musclesWanted_split:
# print(mu)
if mu == musc.getName():
# print(musc.getName())
# print(mu)
getrid = False
if getrid:
trimmuscles.remove(musc)
count +=1
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
# print(fo.getName())
if 'reserve' not in fo.getName() and 'lumbar' not in fo.getName():
getrid = True
for mu in musclesWanted_split:
if mu == fo.getName():
getrid = False
if getrid:
trimforces.remove(f-count)
count += 1
# model should only have muscles that we want now.
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
###
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
return jray
def getKneeContactributions01_wt1(trialdir, musclesWanted_split, tag):
# os.chdir(trialdir)
# solution = osim.MocoTrajectory('muscle_statetrack_grfprescribe_solution_100con.sto')
# model = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# # attempting with just setting muscles to not apply force
# muscles = model.getMuscles()
# for m in range(muscles.getSize()):
# musc = muscles.get(m)
# muscname = musc.getName()
# if muscname not in musclesWanted_split:
# musc.setMaxIsometricForce(0.0)
# # else:
# # print(muscname)
# model.initSystem()
if musclesWanted_split == []:
statesStorage = osim.Storage('muscletrack_states_100con01_wt1.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con01_wt1.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con01_wt1.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor = osim.ModelProcessor('post_simple_model_all_the_probes_muscletrack.osim')
trimmodelprocessor.append(osim.ModOpRemoveMuscles())
trimmodel = trimmodelprocessor.process()
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel_' + tag + '.osim')
initTime = np.array(statesTable.getIndependentColumn())[0]
finalTime = np.array(statesTable.getIndependentColumn())[-1]
# now try the positionMotion
# pomostorage = osim.Storage('trimmingStates2_inter.sto')
pomostorage = osim.Storage('trimmingStates_' + tag + '.sto')
pomotraj = osim.StatesTrajectory.createFromStatesStorage(trimmodel, pomostorage)
pomo = osim.PositionMotion.createFromStatesTrajectory(trimmodel, pomotraj)
trimmodel.addComponent(pomo)
trimmodel.initSystem()
trimmodel.printToXML('trimmingmodel2' + tag + '.osim')
# call the analyze tool to actually do the analysis and get the values.
jray = computeKneeContact(trimmodel, initTime, finalTime, trialdir, tag)
else:
statesStorage = osim.Storage('muscletrack_states_100con01_wt1.sto')
statesTable = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
stateslabels = statesTable.getColumnLabels()
statesTableTrim = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
statesTableTrim2 = osim.TimeSeriesTable('muscletrack_states_100con01_wt1.sto')
# musclesWanted_split = ['1'2'3'4']
# get a trimmed set of states that is just the joint angles speeds, and whatever muscles you want.
for stat in stateslabels:
if 'forceset' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want this one
# print(stat)
getrid = False
if getrid:
statesTableTrim.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim, 'trimmingStates_' + tag + '.sto')
for stat in stateslabels:
if 'forceset' in stat or 'speed' in stat:
getrid = True
for want in musclesWanted_split:
if want in stat:
# want to keep this one
# print(stat)
getrid = False
if getrid:
statesTableTrim2.removeColumn(stat)
osim.STOFileAdapter.write(statesTableTrim2, 'trimmingStates2_' + tag + '.sto')
# get a version of the controls that matches.
controlsTable = osim.TimeSeriesTable('muscletrack_controls_100con01_wt1.sto')
controlslabels = controlsTable.getColumnLabels()
controlsTableTrim = osim.TimeSeriesTable('muscletrack_controls_100con01_wt1.sto')
# get a version of the controls that is trimmed down.
for con in controlslabels:
if 'reserve' not in con and 'lumbar' not in con:
getrid = True
for want in musclesWanted_split:
if want in con:
# want this
# print(con)
getrid = False
if getrid:
controlsTableTrim.removeColumn(con)
osim.STOFileAdapter.write(controlsTableTrim, 'trimmingControls_' + tag + '.sto')
# get a version of the model with no muscles in it
# muscmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
trimmodel = osim.Model('post_simple_model_all_the_probes_muscletrack.osim')
# get rid of muscles that we don't want
trimmuscles = trimmodel.getMuscles()
numMuscles = trimmuscles.getSize()
count = 0
for m in range(numMuscles):
musc = trimmuscles.get(m-count)
# print(musc.getName())
getrid = True
for mu in musclesWanted_split:
# print(mu)
if mu == musc.getName():
# print(musc.getName())
# print(mu)
getrid = False
if getrid:
trimmuscles.remove(musc)
count +=1
# now have to do it for the forceset too?
trimforces = trimmodel.getForceSet()
numForces = trimforces.getSize()
count = 0
for f in range(numForces):
fo = trimforces.get(f-count)
# print(fo.getName())
if 'reserve' not in fo.getName() and 'lumbar' not in fo.getName():
getrid = True
for mu in musclesWanted_split:
if mu == fo.getName():
getrid = False