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from tvb .simulator .lab import *
import threading
import numpy
import time
import sys
from matplotlib .tri import Triangulation
from matplotlib import pyplot as plt
class SimThread (threading .Thread ):
def set_sim (self , sim , ** kwds ):
self .sim = sim
self .kwds = kwds
self .t = - 1.0
def run (self ):
"Convenience method to call the simulator with **kwds and collect output data."
tic = time .time ()
ts , xs = [], []
for _ in self .sim .monitors :
ts .append ([])
xs .append ([])
for data in self .sim (** self .kwds ):
for tl , xl , t_x in zip (ts , xs , data ):
if t_x is not None :
t , x = t_x
if t > self .t :
self .t = t
tl .append (t )
xl .append (x )
for i in range (len (ts )):
ts [i ] = numpy .array (ts [i ])
xs [i ] = numpy .array (xs [i ])
self .results = list (zip (ts , xs ))
self .wall_time = time .time () - tic
def formattime (eta ):
m = 60
h = m * 60
d = 24 * h
msg = ''
if eta > d :
msg += '%d day(s), %d hour(s)' % (eta / d , ((eta / h ) % 24 ))
elif eta > h :
msg += '%d hour(s), %d minute(s)' % (eta / h , ((eta / m ) % 60 ))
else :
msg += '%d minute(s), %d seconds(s)' % (eta / m , eta % m )
return msg
def pbpct (p = 1e2 , eta = None , walltime = None ):
i = int (p / 2 )
msg = '\r [%s%s] %d %%' % ('.' * i , ' ' * (50 - i ), p )
if eta :
msg += ', ETA: ' + formattime (eta )
elif walltime :
msg += ' Wall Time: ' + formattime (walltime )
sys .stdout .write (msg )
sys .stdout .flush ()
def run_sim_with_progress_bar (sim , simulation_length , polltime = 1 ):
tic = time .time ()
ar = SimThread ()
ar .set_sim (sim , simulation_length = simulation_length )
ar .start ()
while True :
prog = ar .t
pct = prog * 1e2 / simulation_length
toc = time .time () - tic
if pct > 0.0 :
time_per_centile = toc / pct
centiles_left = 100 - pct
pbpct (pct , centiles_left * time_per_centile )
else :
pbpct (0.0 )
time .sleep (polltime )
if hasattr (ar , 'wall_time' ):
pbpct (100.0 , walltime = ar .wall_time )
break
return ar .results
cortex = cortex .Cortex (load_default = True )
def multiview (data , suptitle = '' , figsize = (15 , 10 ), ** kwds ):
cs = cortex
vtx = cs .vertices
tri = cs .triangles
rm = cs .region_mapping
x , y , z = vtx .T
lh_tri = tri [(rm [tri ] < 38 ).any (axis = 1 )]
lh_vtx = vtx [rm < 38 ]
lh_x , lh_y , lh_z = lh_vtx .T
lh_tx , lh_ty , lh_tz = lh_vtx [lh_tri ].mean (axis = 1 ).T
rh_tri = tri [(rm [tri ] >= 38 ).any (axis = 1 )]
rh_vtx = vtx [rm < 38 ]
rh_x , rh_y , rh_z = rh_vtx .T
rh_tx , rh_ty , rh_tz = vtx [rh_tri ].mean (axis = 1 ).T
tx , ty , tz = vtx [tri ].mean (axis = 1 ).T
views = {
'lh-lateral' : Triangulation (- x , z , lh_tri [argsort (lh_ty )[::- 1 ]]),
'lh-medial' : Triangulation (x , z , lh_tri [argsort (lh_ty )]),
'rh-medial' : Triangulation (- x , z , rh_tri [argsort (rh_ty )[::- 1 ]]),
'rh-lateral' : Triangulation (x , z , rh_tri [argsort (rh_ty )]),
'both-superior' : Triangulation (y , x , tri [argsort (tz )]),
}
def plotview (i , j , k , viewkey , z = None , zlim = None , zthresh = None , suptitle = '' , shaded = True , cmap = plt .cm .coolwarm , viewlabel = False ):
v = views [viewkey ]
ax = subplot (i , j , k )
if z is None :
z = rand (v .x .shape [0 ])
if not viewlabel :
axis ('off' )
kwargs = {'shading' : 'gouraud' } if shaded else {'edgecolors' : 'k' , 'linewidth' : 0.1 }
if zthresh :
z = z .copy () * (abs (z ) > zthresh )
tc = ax .tripcolor (v , z , cmap = cmap , ** kwargs )
if zlim :
tc .set_clim (vmin = - zlim , vmax = zlim )
ax .set_aspect ('equal' )
if suptitle :
ax .set_title (suptitle , fontsize = 24 )
if viewlabel :
xlabel (viewkey )
figure (figsize = figsize )
plotview (2 , 3 , 1 , 'lh-lateral' , data , ** kwds )
plotview (2 , 3 , 4 , 'lh-medial' , data , ** kwds )
plotview (2 , 3 , 3 , 'rh-lateral' , data , ** kwds )
plotview (2 , 3 , 6 , 'rh-medial' , data , ** kwds )
plotview (1 , 3 , 2 , 'both-superior' , data , suptitle = suptitle , ** kwds )
subplots_adjust (left = 0.0 , right = 1.0 , bottom = 0.0 , top = 1.0 , wspace = 0 , hspace = 0 )
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