In [1]:

    

import sys
sys.path.insert(0, '..')
import time
import matplotlib.pyplot as plt
%matplotlib inline  
from IPython.display import set_matplotlib_formats
set_matplotlib_formats('pdf', 'png')
plt.rcParams['savefig.dpi'] = 75

plt.rcParams['figure.autolayout'] = False
plt.rcParams['figure.figsize'] = 10, 6
plt.rcParams['axes.labelsize'] = 18
plt.rcParams['axes.titlesize'] = 20
plt.rcParams['font.size'] = 16
plt.rcParams['lines.linewidth'] = 2.0
plt.rcParams['lines.markersize'] = 8
plt.rcParams['legend.fontsize'] = 14

plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = "serif"
plt.rcParams['font.serif'] = "cm"
plt.rcParams['text.latex.preamble'] = "\usepackage{subdepth}, \usepackage{type1cm}"

import numpy as np

from Configuration import Configuration
from MotorUnitPool import MotorUnitPool
from NeuralTract import NeuralTract
from SynapsesFactory import SynapsesFactory


    

In [2]:

    

conf = Configuration('confMNPoolWithNodeAxonsAnsDescendingCommand.rmto')
conf.simDuration_ms = 100 # Here I change simulation duration without changing the Configuration file.


    

In [3]:

    

pools = dict()
pools[0] = MotorUnitPool(conf, 'SOL')
#pools[1] = NeuralTract(conf, 'CMExt')
Syn = SynapsesFactory(conf, pools)
del Syn


    

    




Muscle spindle from muscle SOL built.
Motor Unit Pool SOL built
Synaptic Noise on RC built
All the 0 synapses were built

In [4]:

    

t = np.arange(0.0, conf.simDuration_ms, conf.timeStep_ms)


    

In [5]:

    

axonV = np.zeros((len(t), pools[0].unit[0].compNumber))


tic = time.time()
for i in xrange(0, len(t)-1):
    #pools[1].atualizePool(t[i])
    for j in xrange(len(pools[0].unit)):
        pools[0].iInjected[2*j+1] = 10
    pools[0].atualizeMotorUnitPool(t[i])
    axonV[i,:] = pools[0].unit[0].v_mV
toc = time.time()
print str(toc - tic) + ' seconds'


    

    




151.268265963 seconds

In [6]:

    

pools[0].listSpikes()
plt.figure()
plt.plot(pools[0].poolTerminalSpikes[:, 0],
         pools[0].poolTerminalSpikes[:, 1]+1, '.')


    

    
Out[6]:





[<matplotlib.lines.Line2D at 0x7f403afce4d0>]






    

In [7]:

    

plt.figure()
plt.plot(pools[0].poolSomaSpikes[:, 0],
         pools[0].poolSomaSpikes[:, 1]+1, '.')


    

    
Out[7]:





[<matplotlib.lines.Line2D at 0x7f402fd17a90>]






    

In [8]:

    

plt.figure()
plt.plot(t, axonV[:,0], '-')


    

    
Out[8]:





[<matplotlib.lines.Line2D at 0x7f402def59d0>]






    

In [9]:

    

plt.figure()
plt.plot(t, axonV[:,1], '-')


    

    
Out[9]:





[<matplotlib.lines.Line2D at 0x7f402d919650>]






    

In [10]:

    

plt.figure()
plt.plot(t, axonV, '-')


    

    
Out[10]:





[<matplotlib.lines.Line2D at 0x7f402deb8150>,
 <matplotlib.lines.Line2D at 0x7f402deb8050>,
 <matplotlib.lines.Line2D at 0x7f402deb8ed0>,
 <matplotlib.lines.Line2D at 0x7f402deb8090>,
 <matplotlib.lines.Line2D at 0x7f402deb8910>,
 <matplotlib.lines.Line2D at 0x7f402deb8790>,
 <matplotlib.lines.Line2D at 0x7f402deb8f10>,
 <matplotlib.lines.Line2D at 0x7f402deb8810>,
 <matplotlib.lines.Line2D at 0x7f402df02750>,
 <matplotlib.lines.Line2D at 0x7f402df02250>,
 <matplotlib.lines.Line2D at 0x7f402df023d0>,
 <matplotlib.lines.Line2D at 0x7f402df02710>,
 <matplotlib.lines.Line2D at 0x7f4030039350>,
 <matplotlib.lines.Line2D at 0x7f4030039490>,
 <matplotlib.lines.Line2D at 0x7f402fcfc590>,
 <matplotlib.lines.Line2D at 0x7f402fda5310>,
 <matplotlib.lines.Line2D at 0x7f402fd92290>,
 <matplotlib.lines.Line2D at 0x7f402fcf0c10>,
 <matplotlib.lines.Line2D at 0x7f402fcf05d0>,
 <matplotlib.lines.Line2D at 0x7f402fcf0b10>,
 <matplotlib.lines.Line2D at 0x7f402d96a6d0>,
 <matplotlib.lines.Line2D at 0x7f402fd2b350>,
 <matplotlib.lines.Line2D at 0x7f402fd2b0d0>,
 <matplotlib.lines.Line2D at 0x7f402fd2b8d0>,
 <matplotlib.lines.Line2D at 0x7f402fd2b7d0>,
 <matplotlib.lines.Line2D at 0x7f402fd36c90>,
 <matplotlib.lines.Line2D at 0x7f402fd40690>,
 <matplotlib.lines.Line2D at 0x7f402fd40c50>,
 <matplotlib.lines.Line2D at 0x7f402fd40c90>,
 <matplotlib.lines.Line2D at 0x7f402e28e7d0>,
 <matplotlib.lines.Line2D at 0x7f402fd2be50>,
 <matplotlib.lines.Line2D at 0x7f402e28e250>,
 <matplotlib.lines.Line2D at 0x7f402e28e410>,
 <matplotlib.lines.Line2D at 0x7f402e28e2d0>,
 <matplotlib.lines.Line2D at 0x7f402e28e290>,
 <matplotlib.lines.Line2D at 0x7f402e28e610>,
 <matplotlib.lines.Line2D at 0x7f402e28e4d0>,
 <matplotlib.lines.Line2D at 0x7f402e28e5d0>,
 <matplotlib.lines.Line2D at 0x7f402e28e310>,
 <matplotlib.lines.Line2D at 0x7f402fd9e650>,
 <matplotlib.lines.Line2D at 0x7f402e28e6d0>,
 <matplotlib.lines.Line2D at 0x7f402fd9e350>,
 <matplotlib.lines.Line2D at 0x7f402fd9e090>,
 <matplotlib.lines.Line2D at 0x7f402fd9e450>,
 <matplotlib.lines.Line2D at 0x7f402fd9e510>,
 <matplotlib.lines.Line2D at 0x7f402fd9e3d0>,
 <matplotlib.lines.Line2D at 0x7f402fd50d50>,
 <matplotlib.lines.Line2D at 0x7f402fd50e50>,
 <matplotlib.lines.Line2D at 0x7f402fd50e10>,
 <matplotlib.lines.Line2D at 0x7f402fd504d0>,
 <matplotlib.lines.Line2D at 0x7f402fd9e8d0>,
 <matplotlib.lines.Line2D at 0x7f402fd50190>,
 <matplotlib.lines.Line2D at 0x7f402fd502d0>,
 <matplotlib.lines.Line2D at 0x7f402fd50c50>,
 <matplotlib.lines.Line2D at 0x7f402fd50810>,
 <matplotlib.lines.Line2D at 0x7f402fd50890>,
 <matplotlib.lines.Line2D at 0x7f402fd50590>,
 <matplotlib.lines.Line2D at 0x7f402fd50150>,
 <matplotlib.lines.Line2D at 0x7f402fd507d0>,
 <matplotlib.lines.Line2D at 0x7f402fd50cd0>,
 <matplotlib.lines.Line2D at 0x7f402fd50250>,
 <matplotlib.lines.Line2D at 0x7f402fd50b50>,
 <matplotlib.lines.Line2D at 0x7f402fd50a90>,
 <matplotlib.lines.Line2D at 0x7f402fd50f10>,
 <matplotlib.lines.Line2D at 0x7f402fd50a10>,
 <matplotlib.lines.Line2D at 0x7f402fd49610>,
 <matplotlib.lines.Line2D at 0x7f402fd49710>,
 <matplotlib.lines.Line2D at 0x7f402fd498d0>,
 <matplotlib.lines.Line2D at 0x7f402fd49f50>,
 <matplotlib.lines.Line2D at 0x7f402fd49f10>,
 <matplotlib.lines.Line2D at 0x7f402fd50ed0>,
 <matplotlib.lines.Line2D at 0x7f403072a390>,
 <matplotlib.lines.Line2D at 0x7f403070b550>,
 <matplotlib.lines.Line2D at 0x7f403071e8d0>,
 <matplotlib.lines.Line2D at 0x7f403071e550>,
 <matplotlib.lines.Line2D at 0x7f403071e7d0>,
 <matplotlib.lines.Line2D at 0x7f4030584a90>,
 <matplotlib.lines.Line2D at 0x7f405816a350>,
 <matplotlib.lines.Line2D at 0x7f40307147d0>,
 <matplotlib.lines.Line2D at 0x7f403170ad10>,
 <matplotlib.lines.Line2D at 0x7f403a2a8d50>,
 <matplotlib.lines.Line2D at 0x7f403058f090>,
 <matplotlib.lines.Line2D at 0x7f40306f1310>,
 <matplotlib.lines.Line2D at 0x7f40306f1690>,
 <matplotlib.lines.Line2D at 0x7f4030566a50>,
 <matplotlib.lines.Line2D at 0x7f4030089890>,
 <matplotlib.lines.Line2D at 0x7f4030089490>,
 <matplotlib.lines.Line2D at 0x7f40300893d0>,
 <matplotlib.lines.Line2D at 0x7f4030089110>,
 <matplotlib.lines.Line2D at 0x7f40300890d0>,
 <matplotlib.lines.Line2D at 0x7f403058f4d0>,
 <matplotlib.lines.Line2D at 0x7f4030089050>,
 <matplotlib.lines.Line2D at 0x7f4030466f10>,
 <matplotlib.lines.Line2D at 0x7f40304667d0>,
 <matplotlib.lines.Line2D at 0x7f4030466650>,
 <matplotlib.lines.Line2D at 0x7f4030466690>,
 <matplotlib.lines.Line2D at 0x7f4030466e10>,
 <matplotlib.lines.Line2D at 0x7f40304669d0>,
 <matplotlib.lines.Line2D at 0x7f4030466a50>,
 <matplotlib.lines.Line2D at 0x7f4030466750>,
 <matplotlib.lines.Line2D at 0x7f4030089410>,
 <matplotlib.lines.Line2D at 0x7f4030466990>]






    

In [11]:

    

import matplotlib.pyplot as plt
from matplotlib import gridspec


    

In [12]:

    

fig = plt.figure()
gs = gridspec.GridSpec(10, 5)
h = dict()
for i in xrange(50):
    h[i] = fig.add_subplot(gs[i])
    h[i].plot(t,axonV[:,i])
fig = plt.gcf()


    

In [13]:

    

plt.figure()
plt.plot(t, axonV[:,10], '-')


    

    
Out[13]:





[<matplotlib.lines.Line2D at 0x7f402c536b50>]






    

In [14]:

    

import plotly.plotly as py
import plotly.tools as tls
plotly_fig = tls.mpl_to_plotly( fig )
plot_url = py.plot(plotly_fig)


    

    




---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-14-8340c730ecdc> in <module>()
----> 1 import plotly.plotly as py
      2 import plotly.tools as tls
      3 plotly_fig = tls.mpl_to_plotly( fig )
      4 plot_url = py.plot(plotly_fig)

ImportError: No module named plotly.plotly

In [ ]:

    




    

In [ ]: