def dominanceRankingTotal(self, currentEvent, nApp, domIndex, j, minPred,
diffPred):
dom = []
for i in range(j, nApp):
currentApp = domIndex[i]
signature = self.signatures.keys()[currentApp]
initPath, dist = _ucrdtw.ucrdtw(self.signatures[signature],
currentEvent, 0.1)
path = range(initPath, initPath + len(currentEvent))
signatureChunk = self.signatures.items()[currentApp][1][path]
eventTemp = np.array(currentEvent) >= 0
signatureChunkTemp = signatureChunk[eventTemp]
eventTemp = np.array(currentEvent)[eventTemp]
if len(eventTemp) == 0:
dist = np.sum(currentEvent)
else:
if diffPred[currentApp] < 2:
dist = 0
else:
signatureChunkTemp = np.subtract(signatureChunkTemp,
minPred[currentApp])
dist = np.divide(
np.percentile(
np.abs(np.subtract(eventTemp, signatureChunkTemp)),
95), np.max(self.signatures.items()[currentApp][1])
) # Scaled 95-th percentile distance on signature max value
dom.append(dist)
domIndexNew = np.argsort(dom)
del dom, nApp
toReturn = domIndex[domIndexNew[0] + j]
return toReturn
def calc_distances(self,ex_key):
example=self.example_data[ex_key]
#UCRDTW
z=np.zeros(self.n)
for c,col in enumerate(example):
x=example[col].values[::-1]
z_c=np.array([ucrdtw(df[col].values[::-1], x, 0.20, False)[1] for key, df in self.test_data.iteritems()])
#print col
#print z_c
z=z+self.w[c]*z_c
return z
def dtw_totalVsSig_singleEvent(self, event, signature):
totDistances = list()
totCosts = list()
totPaths = list()
currentEvent = event
initPath, dist = _ucrdtw.ucrdtw(self.signatures[signature],
currentEvent, 0.1)
path = range(initPath, initPath + len(event))
totDistances.append(dist)
totPaths.append(path)
self.totDistances[signature] = np.divide(totDistances, len(totPaths))
self.totPaths[signature] = totPaths
del totDistances, totPaths, currentEvent, path, initPath, dist
def featurize(ts, dat, templates):
"""
Get the features from the raw tennis data
:param ts: numpy array of size (samples,sensor readings) which contains the raw data
:param dat: tuple with start and stop indices to slice data
:return:
:rtype :
"""
s = dat[0]
t = dat[1]
data = ts[s:t, :]
length = 1.0 * len(data[:, 0])
a = np.sqrt(np.sum(np.array(data**2, dtype=float), axis=1))
max_index = np.argmax(a)
max_index = 8
if s - max_index < 0:
s = 16
model1x = sm.OLS(range(1, 9), ts[s + max_index:s + max_index + 8, 0])
model1y = sm.OLS(range(1, 9), ts[s + max_index:s + max_index + 8, 1])
model1z = sm.OLS(range(1, 9), ts[s + max_index:s + max_index + 8, 2])
reg1 = np.array([
model1x.fit().params[0],
model1y.fit().params[0],
model1z.fit().params[0]
])
model2x = sm.OLS(range(1, 9), ts[s + max_index - 8:s + max_index, 0])
model2y = sm.OLS(range(1, 9), ts[s + max_index - 8:s + max_index, 1])
model2z = sm.OLS(range(1, 9), ts[s + max_index - 8:s + max_index, 2])
reg2 = np.array([
model2x.fit().params[0],
model2y.fit().params[0],
model2z.fit().params[0]
])
dist = np.zeros((len(templates)))
for j, template in enumerate(templates):
dist[j] = _ucrdtw.ucrdtw(data, template, 0.5, False)[1]
correlation = np.corrcoef(np.c_[data, a], rowvar=0)
return np.hstack([
np.max(data,axis=0),\
np.min(data,axis=0),np.mean(a),\
np.std(a),\
np.min(a),np.max(a),
reg1,reg2,
np.sign(ts[8,0:2]),
(np.argmax(dat,axis=0)-np.argmin(dat,axis=0))/length,
np.array([correlation[0,1],correlation[0,2],correlation[1,2],correlation[0,3],correlation[1,3],correlation[2,3]]),
dist,
np.sum(np.diff(np.sign(data),axis=0)>0,axis=0)/length,\
np.sum(np.diff(np.sign(data),axis=0)<0,axis=0)/length])
def predict(self, X):
"""
The method predicts over the input data
Args:
Xarr (ndarray<float>): The data to predict over
Returns:
(ndarray<int>) The predictions over the data
"""
X = np.array(X)
out = []
for i in range(X.shape[0]):
loc, dist = _ucrdtw.ucrdtw(self.sequences, X[i,:], 0.05, True)
out.append(self.labels[np.floor(loc/(2.0*X.shape[1]))])
return out
def predict(self, X):
"""
The method predicts over the input data
Args:
Xarr (ndarray<float>): The data to predict over
Returns:
(ndarray<int>) The predictions over the data
"""
X = np.array(X)
out = []
for i in range(X.shape[0]):
loc, dist = _ucrdtw.ucrdtw(self.sequences, X[i, :], 0.05, True)
out.append(self.labels[np.floor(loc / (2.0 * X.shape[1]))])
return out
def ComputeDTW(sample_data, sample_data2):
#Read tsFresh tables for all gestures
sample_data = sample_data.as_matrix()
sample_data2 = sample_data2.as_matrix()
mic_distances = []
for mic in range(1, 5):
#distance, path = dtw(sample_data[:,mic], sample_data2[:,mic], dist=euclidean)
loc, distance = _ucrdtw.ucrdtw(stats.zscore(sample_data[:, mic]),
stats.zscore(sample_data2[:, mic]),
0.05)
#Print results
mic_distances.append(distance)
print "Mic: " + str(mic) + ", distance= " + str(distance)
return mic_distances
def featurize(ts,dat,templates):
"""
Get the features from the raw tennis data
:param ts: numpy array of size (samples,sensor readings) which contains the raw data
:param dat: tuple with start and stop indices to slice data
:return:
:rtype :
"""
#start and stop indices
s=dat[0]
t=dat[1]
#slices the time series
data=ts[s:t,:]
length=1.0*len(data[:,0])
#this handles the edge case in which the swings is at the very end of the collection
#computes total acceleration
a=np.sqrt(np.sum(np.array(data**2,dtype=float),axis=1))
#finds the index which corresponds to the maximum acceleration
max_index=8
model1x=sm.OLS(range(1,9),ts[s:s+max_index,0])
model1y=sm.OLS(range(1,9),ts[s:s+max_index,1])
model1z=sm.OLS(range(1,9),ts[s:s+max_index,2])
reg1=np.array([model1x.fit().params[0],model1y.fit().params[0],model1z.fit().params[0]])
model2x=sm.OLS(range(1,9),ts[s+max_index:t,0])
model2y=sm.OLS(range(1,9),ts[s+max_index:t,1])
model2z=sm.OLS(range(1,9),ts[s+max_index:t,2])
reg2=np.array([model2x.fit().params[0],model2y.fit().params[0],model2z.fit().params[0]])
dist=np.zeros((len(templates)))
for j,template in enumerate(templates):
dist[j]=_ucrdtw.ucrdtw(data, template, 0.5, False)[1]
#cross correlation between each sensor reading
correlation=np.corrcoef(np.c_[data,a],rowvar=0)
return np.hstack([
np.max(data,axis=0),\
np.min(data,axis=0),np.mean(a),\
np.std(a),\
np.min(a),np.max(a),
reg1,reg2,#reg3,reg4,
np.sign(ts[8,0:2]),
(np.argmax(dat,axis=0)-np.argmin(dat,axis=0))/length,
np.array([correlation[0,1],correlation[0,2],correlation[1,2],correlation[0,3],correlation[1,3],correlation[2,3]]),
dist,
np.sum(np.diff(np.sign(data),axis=0)>0,axis=0)/length,\
np.sum(np.diff(np.sign(data),axis=0)<0,axis=0)/length])
metavar='DATA_FILE',
type=str,
help='Path to data file')
parser.add_argument('query',
metavar='QUERY_FILE',
type=str,
help='Path to query file')
parser.add_argument('query_size',
metavar='QUERY_SIZE',
type=int,
default=0,
help='Max size of query')
parser.add_argument('warp_width',
metavar='WARP_WIDTH',
type=float,
default=0.05,
help='Width of allowed warp as fraction of query size')
parser.add_argument('-v',
'--verbose',
action='store_true',
default=False,
help='Print verbose info')
args = parser.parse_args()
data = numpy.fromfile(args.data, sep=' ')
query = numpy.fromfile(
args.query,
sep=' ',
count=args.query_size if args.query_size > 0 else -1)
print _ucrdtw.ucrdtw(data, query, args.warp_width, True)
parser.add_argument('warp_width',
metavar='WARP_WIDTH',
type=float,
default=0.05,
help='Width of allowed warp as fraction of query size')
parser.add_argument('curr_ind',
metavar='CURR_IND',
type=int,
default=-1,
help='Current index for self similarity')
parser.add_argument('ez',
metavar='EZ',
type=int,
default=2,
help='Exclusion Zone for self similarity')
parser.add_argument('-v',
'--verbose',
action='store_true',
default=False,
help='Print verbose info')
args = parser.parse_args()
data = numpy.fromfile(args.data, sep=' ')
query = numpy.fromfile(
args.query,
sep=' ',
count=args.query_size if args.query_size > 0 else -1)
print(
_ucrdtw.ucrdtw(data, query, args.warp_width, args.curr_ind, args.ez,
True))
import _ucrdtw
import sys
import numpy as np
import matplotlib.pyplot as plt
import math
if __name__ == '__main__':
data = np.cos(np.linspace(0.0, math.pi * 6, 600)) + (np.random.uniform(-0.5, 0.5, 600) / 10)
query = np.sin(np.linspace(0.0, math.pi * 2, 200))
plt.figure()
plt.plot(data)
plt.plot(query)
loc, dist = _ucrdtw.ucrdtw(data, query, 0.05, True)
query = np.concatenate((np.linspace(0.0, 0.0, loc), query))
plt.plot(query)
plt.show()
import _ucrdtw
import sys
import numpy as np
import matplotlib.pyplot as plt
import math
if __name__ == '__main__':
data = np.cos(np.linspace(0.0, math.pi * 6,
600)) + (np.random.uniform(-0.5, 0.5, 600) / 10)
query = np.sin(np.linspace(0.0, math.pi * 2, 200))
plt.figure()
plt.plot(data)
plt.plot(query)
loc, dist = _ucrdtw.ucrdtw(data, query, 0.05, True)
query = np.concatenate((np.linspace(0.0, 0.0, loc), query))
plt.plot(query)
plt.show()
text_file.write("\n" + str(amp + 1) + "," + str(window + 1) +
",ftw," + str(ftwdistance) + "," +
str(timet.microseconds) + ',' +
str(ftwpath[1][0] + count) + ',' +
str(ftwpath[1][-1] + count))
path1 = np.savetxt('paths/' + "amp_" + str(amp + 1) + "_window_" +
str(window + 1) + '_query_ftw.txt',
ftwpath[0],
delimiter=',')
path2 = np.savetxt('paths/' + "amp_" + str(amp + 1) + "_window_" +
str(window + 1) + '_ref_ftw.txt',
ftwpath[1],
delimiter=',')
#ucrdtw
timeb = datetime.now()
ucrloc, ucrdist = _ucrdtw.ucrdtw(y, x, 0.05)
timet = datetime.now() - timeb
print("ucr complete on amp " + str(amp + 1))
with open("bench_log.txt", "a") as text_file:
text_file.write("\n" + str(amp + 1) + "," + str(window + 1) +
",ucr," + str(ucrdist) + "," +
str(timet.microseconds) + ',' +
str(ucrloc + count) + ',' + str(ucrloc + count))
with open(
'paths/' + str(amp + 1) + "," + str(window + 1) +
'_loc_ucr.txt', "w") as text_file:
text_file.write(str(ucrloc))
#cydtw
timeb = datetime.now()
cdtw_master = pydtw.dtw(
x,
def use_dtw(signal, chunk):
signal_x=signal.axes_data[0]
chunk_x=chunk.axes_data[0]
index, dist = dtw.ucrdtw(signal_x, chunk_x, 0.05, False)
return index, dist
def calc_dtw(scrappie_df_1, scrappie_df_2, warp_width=0.1):
_, dtw_dist = ucrdtw(scrappie_df_1, scrappie_df_2, warp_width, False)
dtw_dist = np.float32(dtw_dist)
return dtw_dist
def transform_dist(x, y, row):
index, dist = dtw.ucrdtw(x[row].values, y[row].values,
0.05, False)
return dist
import _ucrdtw
import numpy
import sys
import argparse
import time
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Calculate best DTW location and distance")
parser.add_argument("data", metavar="DATA_FILE", type=str, help="Path to data file")
parser.add_argument("query", metavar="QUERY_FILE", type=str, help="Path to query file")
parser.add_argument("query_size", metavar="QUERY_SIZE", type=int, default=0, help="Max size of query")
parser.add_argument(
"warp_width",
metavar="WARP_WIDTH",
type=float,
default=0.05,
help="Width of allowed warp as fraction of query size",
)
parser.add_argument("-v", "--verbose", action="store_true", default=False, help="Print verbose info")
args = parser.parse_args()
data = numpy.fromfile(args.data, sep=" ")
query = numpy.fromfile(args.query, sep=" ", count=args.query_size if args.query_size > 0 else -1)
print _ucrdtw.ucrdtw(data, query, args.warp_width, True)