def main():
#Load the filenames
dynamic_trial, static_trial, vsk_file, outputfile = getfilenames()
#Load a dynamic trial, static trial, and vsk (subject measurements)
motionData, vskData, staticData = loadData(dynamic_trial, static_trial,
vsk_file)
#Calculate the static offsets
flat_foot = False
calibratedMeasurements = pycgmStatic.getStatic(staticData, vskData,
flat_foot)
#Calculate the dynamic trial
# passing the calibrated subject measurements
motionData = motionData[:500] #temporary, just to speed up the calculation
result = pycgmCalc.calcAngles(motionData,
start=None,
end=None,
vsk=calibratedMeasurements,
splitAnglesAxis=False,
formatData=False)
#Write the results to a csv file, if wanted,
# otherwise could just return the angles/axis to some other function
pycgmIO.writeResult(result, outputfile)
return
def main(argv):
"""
Take in motion data file, time span
returns output file of angles
pyCGM.py -i <motionFile> -o <outputfile> -s <start> -e <end>
"""
flat_foot = False
global vskdata
start,end = None,None
try:
opts, args = getopt.getopt(argv,"h:i:o:s:e:v:x",["ifile=","ofile=","start=","end=","vskfile=","staticinput="])
except getopt.GetoptError:
print 'pyCGM.py -i <motionFile> -o <outputfile> -s <start> -e <end>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'pyCGM.py -i <motionFile> -o <outputfile> -s <start> -e <end>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-s", "--start"):
start = int(arg)
elif opt in ("-e", "--end"):
end = int(arg)
elif opt in ("-v","--vskfile"):
inputvsk = arg
elif opt in ("-x","--staticinput"):
staticfile = arg
#TODO -x is not working for input
filename = './'+inputfile
motionData = pycgmIO.loadData(filename)
if len(motionData) == 0 or motionData == None:
print "No Data Loaded"
sys.exit()
if inputvsk != None:
vskdata = pycgmIO.loadVSK(inputvsk)
if vskdata!=None:
vsk = pycgmIO.createVskDataDict(vskdata[0],vskdata[1])
if staticfile != None:
staticData = pycgmIO.loadData(staticfile)
calibratedMeasurements = pycgmStatic.getStatic(staticData,vsk,flat_foot)
result=pycgmCalc.calcAngles(motionData,start=start,end=end,vsk=calibratedMeasurements,splitAnglesAxis=False,formatData=False)
pycgmIO.writeResult(result,outputfile)
sys.exit()
def mainMPI(argv):
testtime = time.strftime("%d_%H_%M_%S", time.gmtime())
runfolder = str(testtime) + '/'
pycgmIO.make_sure_path_exists(runfolder)
try:
opts, args = getopt.getopt(argv, "h:i:o:s:e:c:f:p:v:x:r", [
"ifile=", "ofile=", "start=", "end=", "calctype=", "singleframe=",
"nprocs=", "vskfile=", "staticinput=", "rank="
])
except getopt.GetoptError:
print 'pyCGM.py -i <motionFile> -o <outputfile> -s <start> -e <end> -c <calctype> -sf <singleframe>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'pyCGM.py -i <motionFile> -o <outputfile> -s <start> -e <end> -c <calctype> -sf <singleframe> -p <procs>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-s", "--start"):
start = int(arg)
elif opt in ("-e", "--end"):
end = int(arg)
elif opt in ("-c", "--calctype"):
calctype = arg
elif opt in ("-f", "--singleframe"):
singleframe = arg
elif opt in ("-p", "--nprocs"):
procs = int(arg)
elif opt in ("-v", "--vskfile"):
inputvsk = arg
elif opt in ("-x", "--staticinput"):
staticfile = arg
elif opt in ("-r", "--rank"):
rank = arg
#Get this processes rank and the size of the mpi rank call
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
rank_size = comm.Get_size()
#Set the variable motiondata to none at start for all ranks
motiondata = None
vsk = None
static = None
motiondata_lab = None
if rank == 0:
#File to use in calculation
start = 0
flat_foot = False
filename = './' + inputfile
#Time setup
totalTime = time.time()
loadDataTime = time.time()
#Load motion data from file
motionData = pycgmIO.loadData(filename)
loadDataTime = time.time() - loadDataTime
if len(motionData) == 0:
print "No Data Loaded"
sys.exit()
#Load VSK File and parse into dict
if inputvsk != None:
loadVskTime = time.time()
vskdata = pycgmIO.loadVSK(inputvsk)
if vskdata == None:
print "VSK Not Loaded"
vsk = pycgmIO.createVskDataDict(vskdata[0], vskdata[1])
loadVskTime = time.time() - loadVskTime
if staticfile != None:
#Load static file and time it
loadStaticTime = time.time()
staticData = pycgmIO.loadData(staticfile)
loadStaticTime = time.time() - loadStaticTime
#Calculate Static and time it
calculateStaticTime = time.time()
vsk = pycgmStatic.getStatic(staticData, vsk, flat_foot)
calculateStaticTime = time.time() - calculateStaticTime
#Split the motion data to labels and values to send faster with MPI
# then combine again in each process
motiondata_val, motiondata_lab = pycgmIO.splitDataDict(motionData)
#Start timing the calculation time
calculateAnglesTime = time.time()
if rank == 0:
#Split the data evenly for the processes
motionData_val_scatter = []
motionData_val_scatter.append([None])
l = len(motiondata_val) / (rank_size - 1)
for i in range(rank_size - 1):
start = i * l
end = (i + 1) * l
if i == rank_size - 2:
end = len(motiondata_val)
#Append each dataset as an array of the data, vsk info, and static
motionData_val_scatter.append(motiondata_val[start:end])
#Set the master rank single_result value to None so there is a variable
# for it to read when gathering
single_result = None
else:
motionData_val_scatter = []
single_result = None
motionData = comm.scatter(motionData_val_scatter, root=0)
vsk = comm.bcast(vsk, root=0)
static = comm.bcast(static, root=0)
motiondata_lab = comm.bcast(motiondata_lab, root=0)
if rank != 0:
#combine the values and labels back into a dict
motionData = pycgmIO.combineDataDict(motionData, motiondata_lab)
single_result = pycgmCalc.calcFramesMPI(motionData, vsk)
result_total = comm.gather(single_result, root=0)
if rank == 0:
results = np.asarray(result_total)[1:]
#Put all angles in a list instead of separate arrays
angles = []
for i in results:
angles = angles + i
result = angles
#Check the time
calculateAnglesTime = time.time() - calculateAnglesTime
savaDataTime = time.time()
#Write the result to file
angles = ['R Hip', 'L Hip', 'R Knee', 'L Knee', 'R Ankle', 'L Ankle']
axis = [
"PELO", "PELX", "PELY", "PELZ", "HIPO", "HIPX", "HIPY", "HIPZ",
"R KNEO", "R KNEX", "R KNEY", "R KNEZ", "L KNEO", "L KNEX",
"L KNEY", "L KNEZ", "R ANKO", "R ANKX", "R ANKY", "R ANKZ",
"L ANKO", "L ANKX", "L ANKY", "L ANKZ", "R FOOO", "R FOOX",
"R FOOY", "R FOOZ", "L FOOO", "L FOOX", "L FOOY", "L FOOZ"
]
pycgmIO.writeResult(result,
runfolder + outputfile,
axis=axis,
angles=angles)
savaDataTime = time.time() - savaDataTime
totalTimes = time.time() - totalTime
totalTime = totalTimes / 100
with open(runfolder + str(time.time()) + '_Root_Node_Stats.txt',
'wb') as f:
f.write("Total time = %.10fs" % (totalTimes, ) + '\n')
f.write("Cores = " + str(rank_size) + '\n')
f.write(
"Total time to load data \t= %.10fs\t%0.4f%%" %
(loadStaticTime + loadVskTime + loadDataTime,
(loadStaticTime + loadVskTime + loadDataTime) / totalTime) +
'\n')
f.write("\tTime to load VSK = %.10fs\t%0.4f%%" %
(loadVskTime, (loadVskTime) / totalTime) + '\n')
f.write("\tTime to load static data = %.10fs\t%0.4f%%" %
(loadStaticTime, (loadStaticTime) / totalTime) + '\n')
f.write("\tTime to load data = %.10fs\t%0.4f%%" %
(loadDataTime, (loadDataTime) / totalTime) + '\n')
f.write("Total time for calculations \t= %.10fs\t%0.4f%%" %
(calculateStaticTime + calculateAnglesTime,
(calculateStaticTime + calculateAnglesTime) / totalTime) +
'\n')
f.write("\tTime to calculate static = %.10fs\t%0.4f%%" %
(calculateStaticTime,
(calculateStaticTime) / totalTime) + '\n')
f.write("\tTime to calculate angles = %.10fs\t%0.4f%%" %
(calculateAnglesTime,
(calculateAnglesTime) / totalTime) + '\n')
f.write("Total time to save output \t= %.10fs\t%0.4f%%" %
(savaDataTime, (savaDataTime) / totalTime) + '\n')
sys.exit()