duration = min(durations)
windowSize = 60
velWindow = np.arange(600, duration, windowSize)
startshock = 15 * 60
endshock = 30 * 60 + 30 * 2
eVelocity = np.zeros((len(e_shock), len(velWindow) - 1))
cVelocity = np.zeros((len(c_shock), len(velWindow) - 1))
for i in range(len(velWindow) - 1):
startT = velWindow[i]
endT = velWindow[i + 1]
for exp in range(len(e_shock)):
[expVel, et] = aba.getVelRaw(e_shock[exp], tRange=(startT, endT), smoothWinLen=sm)
eVelocity[exp, i] = np.median(expVel)
for cnt in range(len(c_shock)):
[cntVel, ct] = aba.getVelRaw(c_shock[cnt], tRange=(startT, endT), smoothWinLen=sm)
cVelocity[cnt, i] = np.median(cntVel)
fig = pylab.figure(100, figsize=(6.5, 6))
pylab.clf()
pylab.suptitle("Fish velocity traces during shocking")
ax = pylab.subplot(111)
for i in range(len(eVelocity)):
xax = velWindow[1:]
pylab.plot(xax, eVelocity[i], "k", alpha=0.3)
# pylab.plot(xax,eVelocity[i])
pylab.plot(xax, eVelocity[1], "g", lw=3)
pylab.plot(xax, eVelocity[2], "b", lw=3)
frametime = tracking[:,0]
mintime = max(frametime)-min(frametime)
return mintime
#velocity analysis for shock periods, last n min, covering different acclimation times
n=5
minutes = n * 60
e_maxtimes = []
for n in range(len(e_shockR)):
mtime = getmintime(e_shockR[n])
e_maxtimes.append(mtime)
e_mintimes = [x - minutes for x in e_maxtimes]
eBaseVelEnd = []
for n in range(len(e_shockR)):
velocity = aba.getVelRaw(e_shockR[n], (e_mintimes[n], e_maxtimes[n]))
eBaseVelEnd.append(np.median(velocity))
c_maxtimes = []
for n in range(len(c_shockR)):
mtime = getmintime(c_shockR[n])
c_maxtimes.append(mtime)
c_mintimes = [x - minutes for x in c_maxtimes]
cBaseVelEnd = []
for n in range(len(c_shockR)):
cvelocity = aba.getVelRaw(c_shockR[n], (c_mintimes[n], c_maxtimes[n]))
cBaseVelEnd.append(np.median(cvelocity))
#velocity locomation analysis
eBaseVelStart1 = aba.getVelMulti(e_shockR, (0,450))
mintime = max(frametime)-min(frametime)
return mintime
#velocity analysis for shock periods, last n min, covering different acclimation times
n=15
minutes = n * 60
sm = 15; #smooth over 15 frames
e_maxtimes = []
for n in range(len(e_shock)):
mtime = getmintime(e_shock[n])
e_maxtimes.append(mtime)
e_mintimes = [x - minutes for x in e_maxtimes]
eShockVel = []
for n in range(len(e_shock)):
velocity = aba.getVelRaw(e_shock[n], tRange=(e_mintimes[n], e_maxtimes[n]),smoothWinLen=sm)
eShockVel.append(np.median(velocity))
c_maxtimes = []
for n in range(len(c_shock)):
mtime = getmintime(c_shock[n])
c_maxtimes.append(mtime)
c_mintimes = [x - minutes for x in c_maxtimes]
cShockVel = []
for n in range(len(c_shock)):
cvelocity = aba.getVelRaw(c_shock[n], tRange=(c_mintimes[n], c_maxtimes[n]),smoothWinLen=sm)
cShockVel.append(np.median(cvelocity))
#velocity analysis for starting shock periods, last m min, covering different acclimation times
m=15
