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plotsdf.py
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plotsdf.py
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'''
Code for plotting the glomerular activity.
by Esin Yavuz
University of Sussex
email: [email protected]
'''
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import rcParams
import sys
colors= ['r', 'g', 'b', 'y','k','c','m','orange','violet','teal','brown','grey','olive','palegreen','pink','purple']
#Listof all glomeruli that we want.
glomeruli=[15,17,18,19,21,23,
24,25,27,28,29,30,
33,35,36,37,38,39,
42,43,47,48,49,52,
60,62,108,121,135,142]#need to be ordered
glomeruli_toplot=[15,17,23]#need to be ordered
fig_width = 12.0
fig_height = 5.25
fig_size = [fig_width, fig_height] #in inches
params = {'backend': 'SVG', #change to SVG for vector. or GDK for gimp finishing
'axes.labelsize': 12,
'axes.titlesize': 12,
'axes.edgecolor': 'k',
'font.size': 12,
'text.usetex': 'true',
'figure.figsize': fig_size,
'savefig.dpi': 600,
'font.family': 'arial',
'axes.linewidth': 1.2,
'axes.facecolor': 'white',
'lines.linewidth': 2.0,
'lines.markersize': 2.5,
'lines.markeredgewidth': 0.5,
'legend.numpoints': 1,
'legend.columnspacing':1.0,
'legend.labelspacing' : 0.15,
'grid.linestyle':'.',
'grid.linewidth': 0.5,
'grid.color':'lightgrey',
'patch.linewidth': 0,
'svg.fonttype': 'path'
}
rcParams.update(params)
nAL=150
inglom = 5 #also 1 interneuron from LN
sdffile=open('sdffile')#this is the file created by tools/st2asdf_mult
sdfarray = []
for line in sdffile.readlines():
a=line.split(" ")
pt = []
for k in range(len(a)-1):
pt.append(a[k]) # #neurons
sdfarray.append(pt)
sdfnp=np.array(sdfarray,dtype=float)
sdfnp[:,0]=sdfnp[:,0]/1000
sdfnp[:,1:]=sdfnp[:,1:]*1000
print(np.shape(sdfnp))
numrow = 5
numcol = 6
ymax=140
ymin=-10
xmin=0
xmax=sdfnp[-1,0]
print('xmax: ',xmax)
plt.figure(1)
########################
protofile=open('protofile')#This is the modelname.proto file
stimdur=[]
stimid=[]
for line in protofile:
a=line.split(" ")
#following could break down if stim on/off is not in order
if (a[1] == 'odor'):
if (a[5] == '1\n'):
tmparr=[]
tmparr.append(a[0])
if (a[5] == '-1\n'):#&&(len(a)==0)
tmparr.append(a[0])
stimdur.append(tmparr)
stimid.append(int(a[3]))
stimdurnp=np.array(stimdur,dtype=float)
stimdurnp=stimdurnp/1000
####################
toplot_cntr=0
parr = []
for p in np.arange(1,12):
ax=plt.subplot(4,3,p)
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
for kind in range(np.shape(stimdurnp)[0]):
ax.axvspan(stimdurnp[kind,0],stimdurnp[kind,1],color=colors[stimid[kind]])
ax.set_ylim(ymin, ymax)
ax.set_xlim(xmin, xmax)
if (p %3 !=1):
ax.set_yticklabels([])
for neuron in range(nAL):
if (toplot_cntr<3):
glomid = int (neuron / 5)
print(toplot_cntr,glomid)
if (glomeruli_toplot[toplot_cntr]==glomeruli[glomid]):
if (neuron % 5 != 0):
ax=plt.subplot(4,3,toplot_cntr+1)
ax.plot(sdfnp[:,0],sdfnp[:,neuron+1],color='k')
ax.set_ylim(ymin, ymax)
ax.set_xlim(xmin, xmax)
else:
ax=plt.subplot(4,3,toplot_cntr+1)
ax.plot(sdfnp[:,0],sdfnp[:,neuron+1],color='g',zorder=10)
ax.set_ylim(ymin, ymax)
ax.set_xlim(xmin, xmax)
ax.set_title(glomeruli[glomid])
if (neuron % 5 == 4):
toplot_cntr=toplot_cntr+1
parr.append(glomid)
if (glomid %3 !=0):
ax.set_yticklabels([])
if (int(glomid/3)!=4):
ax.set_xticklabels([])
ax=plt.subplot(4,3,10)
ax.plot(sdfnp[:,0],sdfnp[:,sdfnp.shape[1]-2],color='k')
ax.set_xlim(xmin, xmax)
ax.set_ylim(-1.5, 12)
ax=plt.subplot(4,3,11)
ax.plot(sdfnp[:,0],sdfnp[:,sdfnp.shape[1]-1],color='k')
ax.set_xlim(xmin, xmax)
ax.set_ylim(-1.5, 12)
ax.set_xlim(xmin, xmax)
print('xmax 1: ',xmax)
##############################
cmpfile=open('cmpfile')#this is the outputfile (outname/outname.out.cmp)
cmparray = []
for line in cmpfile.readlines():
a=line.split(" ")
pt = []
for k in range(len(a)-1):
pt.append(a[k]) # #neurons
cmparray.append(pt)
cmpnp=np.array(cmparray,dtype=float)
cmpnp[:,0]=cmpnp[:,0]/1000
xmin=0
xmax=cmpnp[-1,0]
print('xmax 2: ',xmax)
for p in range(6):
ax=plt.subplot(4,3,4+p)
ax.set_xticklabels([])
ax.set_xlim(xmin, xmax)
ax.set_ylim(-1e-11, 5e-11)
for p in [7,8,9]:
ax=plt.subplot(4,3,p)
ax.set_ylim(15, 35)
ax=plt.subplot(4,3,4)
ax.set_ylabel('p ')
ax.plot(cmpnp[:,0],cmpnp[:,1],color='k') # glom 0
ax=plt.subplot(4,3,5)
ax.plot(cmpnp[:,0],cmpnp[:,4],color='k') # glom 1
ax=plt.subplot(4,3,6)
ax.plot(cmpnp[:,0],cmpnp[:,5],color='k') # glom 5
ax=plt.subplot(4,3,7)
ax.set_ylabel('g (pS)')
ax.plot(cmpnp[:,0],cmpnp[:,2]/1e-6,color='k')
ax=plt.subplot(4,3,8)
ax.plot(cmpnp[:,0],cmpnp[:,7]/1e-6,color='k')
ax=plt.subplot(4,3,9)
ax.plot(cmpnp[:,0],cmpnp[:,8]/1e-6,color='k')
for p in np.arange(4,10):
ax=plt.subplot(4,3,p)
ax2 = ax.twinx()
ax2.plot(cmpnp[:,0],cmpnp[:,3],color='#445566',linewidth=1.5)
ax2.yaxis.tick_right()
ax2.spines['right'].set_visible(False)
ax2.spines['top'].set_visible(False)
ax2.xaxis.set_ticks_position('bottom')
if (p %3 !=0):
ax2.set_yticklabels([])
title= sys.argv[1]
print(title)
ax=plt.subplot(4,3,11)
ax.set_xlabel('time (s)')
ax=plt.subplot(4,3,1)
ax.set_ylabel("spike density (Hz)")
ax=plt.subplot(4,3,10)
ax.set_ylabel("spike density (Hz)")
plt.text(2,61.25,"glomerulus:")
plt.text(223.5,23.9,'reward',rotation=270)
plt.text(223.5,40.1,'reward',rotation=270)
plt.text(1,58,"A+",fontsize=11)
plt.text(9,58,"A+",fontsize=11)
plt.text(17,58,"A+",fontsize=11)
plt.text(25,58,"A+",fontsize=11)
plt.text(33,58,"A+",fontsize=11)
plt.text(41.1,58,"B-",fontsize=11)
plt.text(49,58,"A+",fontsize=11)
plt.text(57,58,"A+",fontsize=11)
plt.text(65,58,"A+",fontsize=11)
plt.text(-20,60.5,'a',fontsize=14)
plt.text(-20,42.1,'b',fontsize=14)
plt.text(-20,26.7,'c',fontsize=14)
plt.text(-20,10,'d',fontsize=14)
plt.text(2,10,'learner',fontsize=12)
plt.text(78,10,'non-learner',fontsize=12)
plt.subplots_adjust(left=0.09,right=0.95,bottom=0.1,top=0.93,wspace=0.08,hspace=0.2)
plt.show()