"""
wscale.py
Code to analyze and calculate the scaling of weights as a function of input dendritic location
Contributors: salvadordura@gmail.com
"""
import utils
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import interp1d
from cycler import cycler
import sys, os
def calculateEPSPs(params, data, somaLabel='soma', stimRange=[3000,4000], syn='exc'):
out = {}
secs = [s for s in params[0]['values']]
locs = [s for s in params[1]['values']]
for key, d in data.items():
cellLabel = d['simData']['V_soma'].keys()[0]
vsoma = d['simData']['V_'+somaLabel][cellLabel]
if syn == 'exc':
epsp = max(vsoma[stimRange[0]:stimRange[1]]) - vsoma[stimRange[0]-1] # max voltage between stim time - baseline
elif syn == 'inh':
epsp = min(vsoma[stimRange[0]:stimRange[1]]) - vsoma[stimRange[0]-1] # min voltage between stim time - baseline
seg = (d['paramValues'][0], d['paramValues'][1])
weight = d['paramValues'][1]
print(seg, weight, epsp, len(vsoma))
out[tuple(seg)].append([weight, epsp])
return out
def calculateEPSPsPops(params, data, somaLabel='soma', stimRange=[3000,4000], syn='exc'):
out = {}
pops = [p for p in params[2]['values']]
secs = [s for s in params[0]['values']]
locs = [s for s in params[1]['values']]
for pop in pops:
out[pop] = {}
for sec,loc in zip(secs,locs): out[pop][(sec,loc)] = []
for key, d in data.items():
cellLabel = list(d['V_soma'].keys())[0] # d['simData']['V_soma'].keys()[0]
vsoma = d['V_'+somaLabel][cellLabel] #d['simData']['V_'+somaLabel][cellLabel]
if syn == 'exc':
epsp = max(vsoma[stimRange[0]:stimRange[1]]) - vsoma[stimRange[0]-1] # max voltage between stim time - baseline
elif syn == 'inh':
epsp = min(vsoma[stimRange[0]:stimRange[1]]) - vsoma[stimRange[0]-1] # min voltage between stim time - baseline
pop = d['paramValues'][2]
seg = (d['paramValues'][0], d['paramValues'][1])
weight = d['paramValues'][3]
print(pop, seg, weight, epsp, len(vsoma))
out[pop][tuple(seg)].append([weight, epsp])
return out
def calculateWeightNorm(params, data, epspNorm=0.5, somaLabel='soma', stimRange=[3000,4000], savePath=None):
epsp = calculateEPSPs(params, data, somaLabel=somaLabel, stimRange=stimRange)
segs = [s for s in params[1]['values']]
segs.sort()
weightNorm = {}
for seg in segs: weightNorm[seg[0]] = [] # empty list for each section
for seg in segs:
epspSeg = epsp[tuple(seg)]
epspSeg.sort()
x,y = zip(*epspSeg)
f = interp1d(y,x,fill_value="extrapolate")
w = f(epspNorm)
wnorm = w / epspNorm
weightNorm[seg[0]].append(wnorm)
print('\n%s wscale = %.6f' % (str(seg), wnorm))
if savePath:
import pickle
with open(savePath+'_weightNorm.pkl', 'wb') as fileObj:
pickle.dump(weightNorm, fileObj)
def calculateWeightNormPops(params, data, epspNorm=0.5, somaLabel='soma', stimRange=[3000, 4000], savePath=None,
popSaveLabels ={'IT2': 'IT2_reduced', 'IT4': 'IT4_reduced', 'IT5A': 'IT5A_full', 'IT5B': 'IT5B_reduced',
'PT5B': 'PT_full', 'IT6': 'IT6_reduced', 'CT6': 'CT6_reduced', 'PV2': 'PV_simple', 'SOM2': 'SOM_simple'}):
epsp = calculateEPSPsPops(params, data, somaLabel=somaLabel, stimRange=stimRange)
pops = [p for p in params[2]['values']]
secs = [s for s in params[0]['values']]
locs = [s for s in params[1]['values']]
segs=[]
for sec,loc in zip(secs,locs): segs.append((sec,loc))
segs.sort()
weightNorm = {}
for pop in pops:
print(pop)
weightNorm[pop] = {}
for seg in segs: weightNorm[pop][seg[0]] = [] # empty list for each section
for seg in segs:
epspSeg = epsp[pop][tuple(seg)]
epspSeg.sort()
x,y = zip(*epspSeg)
print(x,y)
f = interp1d(y,x,fill_value="extrapolate")
w = f(epspNorm)
print(w)
wnorm = w / epspNorm
print(wnorm)
weightNorm[pop][seg[0]].append(wnorm)
print('\n%s %s wscale = %.6f' % (pop, str(seg), wnorm))
if savePath:
import pickle
with open(savePath+popSaveLabels[pop]+'_weightNorm.pkl','wb') as fileObj:
pickle.dump(weightNorm[pop], fileObj)
return weightNorm
def plotEPSPs(epsp, dataFolder, batchLabel, addLegend=True, includeSegs = None):
utils.setPlotFormat(numColors = 8)
if len(params) == 3:
pops = ['_']
segs = includeSegs if includeSegs else [s for s in params[0]['values']]
weights = params[2]['values']
epspPops = {'_': epsp}
elif len(params) == 4:
pops = params[2]['values']
segs = includeSegs if includeSegs else epsp[pops[0]].keys() # params[1]['values']
weights = params[3]['values']
epspPops = epsp
for pop in pops:
plt.figure(figsize=((12,8)))
for seg in segs:
if not seg[0].startswith('axon') and seg[1] not in [0.0,1.0]:
epspSeg = epspPops[pop][tuple(seg)]
if epspSeg:
epspSeg.sort()
x,y = zip(*epspSeg)
handles = plt.plot(x, y, marker='o', markersize=10, label=str(seg))
plt.xlabel('Weight (of NetStim connection)')
#xtick = np.arange(0.0, 0.0022, 0.0002)
#plt.xticks(xtick, xtick)
plt.ylabel('Somatic EPSP amplitude (mV) in response to 1 NetStim spike')
if addLegend: plt.legend(title = 'Section', loc=2)
if includeSegs:
plt.savefig('%s/%s/%s_%s_epsp_subset.png' % (dataFolder, batchLabel, batchLabel, pop))
else:
plt.savefig('%s/%s/%s_%s_epsp.png' % (dataFolder, batchLabel, batchLabel, pop))
#plt.show()
# main code
if __name__ == '__main__':
# run batch E cells
dataFolder = '../data/'
batchLabels = ['v22_batch13'] #, 'v22_batch19'] #, 'v22_batch1', 'v22_batch16', 'v22_batch17']
loadFromFile = 1
''' run via batch.py
b = batch.weightNormE(pops=['IT2', 'IT4'], rule='IT2_reduced', weight=[0.0001])
b.batchLabel = batchLabel
b.saveFolder = dataFolder+b.batchLabel
b.method = 'grid'
setRunCfg(b, 'mpi')
b.run() # run batch
'''
popSaveLabels = {'IT2': 'IT2_reduced', 'IT3': 'IT3_reduced', 'ITP4': 'ITP4_reduced', 'ITS4': 'ITS4_reduced',
'IT5A': 'IT5A_reduced', 'CT5A': 'CT5A_reduced', 'IT5B': 'IT5B_reduced', 'CT5B': 'CT5B_reduced', 'PT5B': 'PT5B_reduced',
'IT6': 'IT6_reduced', 'CT6': 'CT6_reduced',
'PV2': 'PV_reduced', 'SOM2': 'SOM_reduced', 'VIP2': 'VIP_reduced', 'NGF2': 'NGF_reduced',
'IRE': 'RE_reduced', 'TC': 'TC_reduced', 'HTC': 'HTC_reduced', 'TI': 'TI_reduced'}
# analyze batch E cells
for batchLabel in batchLabels:
params, data = utils.readBatchData(dataFolder, batchLabel, loadAll=loadFromFile, saveAll=1-loadFromFile, vars=[('simData','V_soma')], maxCombs=None)
epsp = calculateEPSPsPops(params, data, somaLabel='soma', stimRange=[10*700,10*800], syn='exc')
plotEPSPs(epsp, dataFolder, batchLabel, addLegend=1)
#plotEPSPs(epsp, dataFolder, batchLabel, addLegend=1, includeSegs=[('apic_28',0.5), ('apic_36',0.5), ('apic_49',0.5), ('apic_56',0.5)])
weightNorm = calculateWeightNormPops(params, data, somaLabel='soma', stimRange=[10*700,10*800], popSaveLabels=popSaveLabels, savePath=dataFolder+'/'+batchLabel+'/')