def loadData(dynamic_trial, static_trial, vsk_file):
#load the data, usually there is some checks in here to make sure we loaded
# correctly, but for now we assume its loaded
motionData = pycgmIO.loadData(dynamic_trial)
vskdata = pycgmIO.loadVSK(vsk_file)
staticData = pycgmIO.loadData(static_trial)
#The vsk is loaded, but for some reasons the return is split, so we combine
vsk = pycgmIO.createVskDataDict(vskdata[0], vskdata[1])
print("Motion Data Length:", len(motionData))
return motionData, vsk, staticData
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 loadData(dynamic_trial, static_trial, vsk_file):
"""Loads the data given the paths to the dynamic trial, the static
trial, and the vsk file. Calls to pycgmIO are made to load in the
data.
Returns
-------
tuple
A tuple of three arrays that pertain to the motion data,
the vsk file, and the static data. These arrays are then directly
used to compute the joint angles. To see how these arrays are
made, please refer to pycgmIO.
"""
#load the data, usually there is some checks in here to make sure we loaded
# correctly, but for now we assume its loaded
motionData = pycgmIO.loadData(dynamic_trial)
vskdata = pycgmIO.loadVSK(vsk_file)
staticData = pycgmIO.loadData(static_trial)
#The vsk is loaded, but for some reasons the return is split, so we combine
vsk = pycgmIO.createVskDataDict(vskdata[0], vskdata[1])
print("Motion Data Length:", len(motionData))
return motionData, vsk, staticData
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()