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# -*- coding: utf-8 -*-
"""
Created on Wed Mar 13 15:21:03 2019
@author: BIEL
"""
import untangle
import matplotlib
import matplotlib.pyplot as plt
import scipy.signal
import copy
import numpy as np
def plotData(data,tag,labels=None, dataRange=None, secondsRange=None,
showDataPlot=True):
total=len(data)
info=[]
for i in range(total): info.append(data[i][tag])
if labels==None:
labels=list(map(lambda x: str(x), list(range(len(info[0])))))
if secondsRange!=None:
dataRange=list(map(lambda x:int(x*60), secondsRange))
if dataRange!=None:
info=info[dataRange[0]:dataRange[1]]
else:
dataRange=[0, len(data)]
separated={}
for i in range(len(info)):
for j in range(len(info[0])):
if i==0:
separated[labels[j]]=[info[i][j]]
else:
separated[labels[j]].append(info[i][j])
t=list(range(dataRange[0],dataRange[1]))
if showDataPlot:
fig=plt.figure()
ax = fig.add_subplot(1, 1, 1)
for i in separated:
ax.plot(t,separated[i], label=i)
plt.show()
return separated
def findClaps(data,tag,n_claps=2,labels=None, dataRange=None, secondsRange=None, spikeSep=10,
showDataPlot=True, drop=None):
separated=plotData(data,tag,labels=labels, dataRange=dataRange, secondsRange=secondsRange,
showDataPlot=showDataPlot)
#lets found the spikes in each data
fcs=[]
for i in separated:
globalMax=max(separated[i])
fc=[]
count=0
factor=0.01
while len(fc)!=n_claps and count<10000:
x=copy.deepcopy(separated[i])
#
# x=list(map(lambda x: x if x>globalMax*factor else globalMax*factor,x))
# x=np.array(x)
# fc=scipy.signal.argrelextrema(x,np.greater,order=10)
fc,_=scipy.signal.find_peaks(x,height=globalMax*factor, distance=spikeSep)
factor*=1.05
if factor>=1:
break
count+=1
fcs.append([i,fc])
n=n_claps
if drop!=None:
if type(drop)==int:
fcs.remove(fcs[drop])
else:
cpfcs=[]
for i in range(len(fcs)):
if i not in drop:
cpfcs.append(fcs[i])
fcs=cpfcs
if not all(len(i[1])==n for i in fcs):
goods=[]
for j in fcs:
if len(j[1])==n:
goods.append(j[1])
if len(goods)==0:
raise ValueError ('no solution')
else:
claps=sum([i for i in goods])
res=[int(i/len(goods)) for i in claps]
else:
claps=sum([i[1] for i in fcs])
res=[int(i/len(fcs)) for i in claps]
res=[res[i]+dataRange[0] for i in range(len(res))]
return res
def get_default_segment_index():
index=['pelvis','l5','l3','t12','t8','neck','head','right_shoulder',
'right_upper_arm','right_forearm','right_hand','left_shoulder',
'left_upper_arm','left_forearm','left_hand','right_upper_leg',
'right_lower_leg','right_foot','right_toe','left_upper_leg',
'left_lower_leg','left_foot','left_toe']
return index
def get_default_sensor_index():
index=['pelvis','t8','head','right_shoulder','right_upper_arm','right_fore_arm',
'right_hand','left_shoulder','left_upper_arm','left_fore_arm', 'left_hand',
'right_upper_leg','right_lower_leg','right_foot',
'left_upper_leg','left_lower_leg','left_foot']
return index
def get_default_joint_index():
index=['L5S1','L4L3','L1T12','T9T8','T1C7','C1Head','RightC7Shoulder',
'RightShoulder','RightElbow','RightWrist','LeftC7Shoulder',
'LeftShoulder','LeftElbow','LeftWrist', 'RightHip','RightKnee',
'RightAnkle','RightBallFoot','LeftHip','LeftKnee','LeftAnkle',
'LeftBallFoot']
index=list(map(lambda x:x+'j',index))
return index
def get_dictionary_from_class(obj):
ll_atrib=dir(obj)
d={}
for attribute in ll_atrib:
d[attribute]=getattr(obj,attribute)
return d
def prepareline(line, tag, index, scaled):
linep=line.split(' ')
# Only the information of sensor, segments or joints pass through this function
#First two lines: segments, 3rd line: sensors,
how_many_info={'position':3, 'orientation':4, 'velocity':3, 'acceleration': 3,
'angularVelocity': 3, 'angularAcceleration':3,
'sensorMagneticField':3,'sensorOrientation': 4, 'sensorFreeAcceleration':3,
'jointAngle':3, 'jointAngleXZY':3,'jointAngleErgo':3,
'centerOfMass':3, 'footContacts':1}
linep=list(map(lambda x: scaled*float(x), linep)) #pass to float
if tag in how_many_info:
n=how_many_info[tag]
else:
s='No tag <'+tag+'> in how_many_info'
raise ValueError (s)
linep=[linep[x:x+n] for x in range(0, len(linep),n)]
if len(linep)!=len(index):
print(index)
s='Error using '+tag
raise ValueError (s)
coord={}
for i in range(len(index)):coord[index[i]]=linep[i]
return coord
class MVNX_Index():
def __init__(self, info, prop=False):
self.segment_index=get_default_segment_index()
self.sensor_index=get_default_sensor_index()
self.joint_index=get_default_joint_index()
self.footContacts_index=['LeftFoot_Heel', 'LeftFoot_Toe','RightFoot_Heel', 'RightFoot_Toe']
self.mass_index=['Center_Of_Mass']
self.ergo_index=['jnt1','jnt2','jnt3','jnt4']
self.info=info
if prop:
for index in [self.segment_index, self.sensor_index, self.joint_index]:
index.append('prop')
def __getitem__(self, tag):
if tag in self.info:
if tag in ['position','orientation','velocity','acceleration',
'angularVelocity', 'angularAcceleration']:
return self.segment_index
elif tag in ['sensorMagneticField','sensorOrientation','sensorFreeAcceleration']:
return self.sensor_index
elif tag in ['jointAngle', 'jointAngleXZY']:
return self.joint_index
elif tag=='jointAngleErgo':
return self.ergo_index
elif tag=='footContacts':
return self.footContacts_index
elif tag=='centerOfMass':
return self.mass_index
else:
return None
class MVNX():
def __init__(self,mvnx_root):
self.root=mvnx_root
self.xml_file=untangle.parse(mvnx_root)
self.frames=self.xml_file.mvnx.subject.frames.frame
self.frames=self.frames[3:]
self.total_frames=len(self.frames)
self.available_info=[i for i in get_dictionary_from_class(self.frames[3])]
self.all_index=MVNX_Index(self.available_info)
self.mvn_version=self.xml_file.mvnx.mvn['version']
self.mvn_build=self.xml_file.mvnx.mvn['build']
self.subject=self.xml_file.mvnx.subject._attributes
def get_info(self,tag, scaled=1):
if tag not in self.available_info:
raise ValueError ('Not available info in MVNX')
else:
ll=[]
for i in range(self.total_frames):
s=getattr(self.frames[i],tag)
s=getattr(s,'cdata')
d=prepareline(s,tag, self.all_index[tag], scaled)
ll.append(d)
return ll
class MVNX_1_PROP():
def __init__(self,mvnx_root):
self.root=mvnx_root
self.xml_file=untangle.parse(mvnx_root)
self.frames=self.xml_file.mvnx.subject.frames.frame
self.frames=self.frames[3:]
self.total_frames=len(self.frames)
self.available_info=[i for i in get_dictionary_from_class(self.frames[3])]
self.all_index=MVNX_Index(self.available_info, prop=True)
self.mvn_version=self.xml_file.mvnx.mvn['version']
self.mvn_build=self.xml_file.mvnx.mvn['build']
self.subject=self.xml_file.mvnx.subject._attributes
def get_info(self,tag, scaled=1):
if tag not in self.available_info:
raise ValueError ('Not available info in MVNX')
else:
ll=[]
for i in range(self.total_frames):
s=getattr(self.frames[i],tag)
s=getattr(s,'cdata')
d=prepareline(s,tag, self.all_index[tag], scaled)
ll.append(d)
return ll
def obtainMVNX(mvnx_root):
mvnx_file=MVNX_1_PROP(mvnx_root)
if mvnx_file.xml_file.mvnx.subject['segmentCount']=='23':
mvnx_file=MVNX(mvnx_root)
return mvnx_file |