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analysis.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Jan 19 14:30:02 2020
@author: Metin Bicer
"""
import os
import opensim as osim
def runAnalysis(modelFileName='Rajagopal2015-scaled.osim',
trials=['GC5_ss1', 'GC5_ss3', 'GC5_ss8', 'GC5_ss9', 'GC5_ss11']):
'''
runs multiple id, so and jr analyses in OpenSim 3.3
Parameters
----------
modelFileName : string
Original (scaled) model filename
trials : list of strings
trial names
'''
# xml folder
xmlFold = '0_xml/'
# data folder
dataFold = '1_data/'
# results folder
resultsFold = 'Results/'
if not os.path.isdir(resultsFold):
os.mkdir(resultsFold)
# model main folder
modelFold = '2_models/'
# original model
originalModelFile = modelFold + modelFileName
osimModel = osim.Model(originalModelFile)
# modified model folders
modelsubFolds = [x[0] for x in os.walk(modelFold)]
modelFileNames = []
modelPaths = []
for fold in modelsubFolds[1:]:
for model in os.listdir(fold):
modelFileNames.append(model)
modelPaths.append(os.path.join(fold, model))
# appended forceset
forcesetFile = xmlFold + '/Forceset.xml'
for trial in trials:
ikFile = dataFold + trial + '.mot'
grfFile = dataFold + trial + '_kinetics.mot'
# read ik and grf
ik = osim.Storage(ikFile)
grf = osim.Storage(grfFile)
trialFold = resultsFold + trial
if not os.path.isdir(trialFold):
os.mkdir(trialFold)
# get the ExternalLoads object to write the exact path of the grfFile
extLoads = osim.ExternalLoads(osimModel, xmlFold + 'ExternalLoads.xml')
extLoads.setDataFileName(grfFile)
extLoads.setExternalLoadsModelKinematicsFileName(ikFile)
extLoads.setLowpassCutoffFrequencyForLoadKinematics(6)
externalLoadsFile = 'ExternalLoads.xml'
# print the external loads under trialFold
extLoads.printToXML(externalLoadsFile)
# run ID
idTool = osim.InverseDynamicsTool(xmlFold+'InverseDynamics.xml')
idTool.setModelFileName(originalModelFile)
idTool.setStartTime(grf.getFirstTime())
idTool.setEndTime(grf.getLastTime())
idTool.setResultsDir(trialFold)
idTool.setCoordinatesFileName(ikFile)
idTool.printToXML('id.xml')
idTool_run = osim.InverseDynamicsTool('id.xml')
idTool_run.run()
# get the SO analysis
soAnalysis = osim.StaticOptimization()
soAnalysis.setStartTime(grf.getFirstTime())
soAnalysis.setEndTime(grf.getLastTime())
# folders
soResultFolder = trialFold + '/SOResults'
jrResultFolder = trialFold + '/JRResults'
# create results folders
if not os.path.isdir(soResultFolder):
os.mkdir(soResultFolder)
if not os.path.isdir(jrResultFolder):
os.mkdir(jrResultFolder)
# create a soTool (this will be updated for each analysis)
soTool = osim.AnalyzeTool()
soTool.getAnalysisSet().adoptAndAppend(soAnalysis)
soTool.setInitialTime(grf.getFirstTime())
soTool.setFinalTime(grf.getLastTime())
forcesetFileStr = osim.ArrayStr()
forcesetFileStr.append(forcesetFile)
soTool.setForceSetFiles(forcesetFileStr)
soTool.setExternalLoadsFileName(externalLoadsFile)
soTool.setCoordinatesFileName(ikFile)
soTool.setLowpassCutoffFrequency(6)
soTool.setResultsDir(soResultFolder)
soTool.setOutputPrecision(15)
# create a jr analysis (this will be updated for each analysis)
jrAnalysis = osim.JointReaction()
jrAnalysis.setName('JR')
jrAnalysis.setStartTime(grf.getFirstTime())
jrAnalysis.setEndTime(grf.getLastTime())
# joint reactions to be calculated for jointNames exerted on
# onBodies and expressed in inFrame
jointNames = osim.ArrayStr()
jointNames.append('all')
onBodies = osim.ArrayStr()
onBodies.append('child')
inFrame = osim.ArrayStr()
inFrame.append('child')
jrAnalysis.setOnBody(onBodies)
jrAnalysis.setInFrame(inFrame)
jrAnalysis.setJointNames(jointNames)
# create a jr tool (this will be updated for each analysis)
jrTool = osim.AnalyzeTool()
jrTool.setResultsDir(jrResultFolder)
jrTool.setInitialTime(grf.getFirstTime())
jrTool.setFinalTime(grf.getLastTime())
jrTool.setExternalLoadsFileName(externalLoadsFile)
jrTool.setCoordinatesFileName(ikFile)
jrTool.setLowpassCutoffFrequency(6)
# set the analysis
jrTool.getAnalysisSet().adoptAndAppend(jrAnalysis)
jrTool.setOutputPrecision(15)
jrTool.setForceSetFiles(forcesetFileStr)
for newModelFile, newModelPath in zip(modelFileNames, modelPaths):
osimModel = osim.Model(newModelPath)
toolNames = osimModel.getName() + '_' + trial
# set soTool attribs depending on this new model
soTool.setName(toolNames)
soTool.setModelFilename(newModelPath)
# print the soTool (prints to the OpenSim installation directory (C:\OpenSim 3.3)
soTool.printToXML('so.xml')
# create a new soTool from the printed xml
soTool_run = osim.AnalyzeTool('so.xml')
soTool_run.run()
# jrAnalysis
jrAnalysis.setForcesFileName(soResultFolder + '/' + toolNames + '_StaticOptimization_force.sto')
# set jrtool attribs depending on this new model
jrTool.setModelFilename(newModelPath)
jrTool.setName(toolNames)
# print the jrTool (prints to the OpenSim installation directory (C:\OpenSim 3.3)
jrTool.printToXML('jr.xml')
# create a new soTool from the printed xml
jrTool_run = osim.AnalyzeTool('jr.xml')
jrTool_run.run()
# remove unnecessary files
os.remove('id.xml')
os.remove('so.xml')
os.remove('jr.xml')
os.remove('ExternalLoads.xml')
if __name__ == "__main__":
runAnalysis()