def createExportNeuroML2(netParams=None,
simConfig=None,
reference=None,
connections=True,
stimulations=True,
output=False):
''' Sequence of commands to create and export network to NeuroML2 '''
import __main__ as top
if not netParams: netParams = top.netParams
if not simConfig: simConfig = top.simConfig
sim.initialize(
netParams,
simConfig) # create network object and set cfg and net params
pops = sim.net.createPops() # instantiate network populations
cells = sim.net.createCells(
) # instantiate network cells based on defined populations
conns = sim.net.connectCells(
) # create connections between cells based on params
stims = sim.net.addStims(
) # add external stimulation to cells (IClamps etc)
simData = sim.setupRecording(
) # setup variables to record for each cell (spikes, V traces, etc)
sim.exportNeuroML2(
reference, connections,
stimulations) # export cells and connectivity to NeuroML 2 format
if output: return (pops, cells, conns, stims, simData)
def load(filename,
simConfig=None,
output=False,
instantiate=True,
createNEURONObj=True):
''' Sequence of commands load, simulate and analyse network '''
import sim
sim.initialize() # create network object and set cfg and net params
sim.cfg.createNEURONObj = createNEURONObj
sim.loadAll(filename,
instantiate=instantiate,
createNEURONObj=createNEURONObj)
if simConfig:
sim.setSimCfg(simConfig) # set after to replace potentially loaded cfg
if len(sim.net.cells) == 0 and instantiate:
pops = sim.net.createPops() # instantiate network populations
cells = sim.net.createCells(
) # instantiate network cells based on defined populations
conns = sim.net.connectCells(
) # create connections between cells based on params
stims = sim.net.addStims(
) # add external stimulation to cells (IClamps etc)
simData = sim.setupRecording(
) # setup variables to record for each cell (spikes, V traces, etc)
if output:
try:
return (pops, cells, conns, stims, simData)
except:
pass
def plotTraces (include = None, timeRange = None, overlay = False, oneFigPer = 'cell', rerun = False,
figSize = (10,8), saveData = None, saveFig = None, showFig = True):
'''
Plot recorded traces
- include (['all',|'allCells','allNetStims',|,120,|,'E1'|,('L2', 56)|,('L5',[4,5,6])]): List of cells for which to plot
the recorded traces (default: [])
- timeRange ([start:stop]): Time range of spikes shown; if None shows all (default: None)
- overlay (True|False): Whether to overlay the data lines or plot in separate subplots (default: False)
- oneFigPer ('cell'|'trace'): Whether to plot one figure per cell (showing multiple traces)
or per trace (showing multiple cells) (default: 'cell')
- rerun (True|False): rerun simulation so new set of cells gets recorded (default: False)
- figSize ((width, height)): Size of figure (default: (10,8))
- saveData (None|True|'fileName'): File name where to save the final data used to generate the figure;
if set to True uses filename from simConfig (default: None)
- saveFig (None|True|'fileName'): File name where to save the figure;
if set to True uses filename from simConfig (default: None)
- showFig (True|False): Whether to show the figure or not (default: True)
- Returns figure handles
'''
print('Plotting recorded cell traces ...')
if include is None: include = [] # If not defined, initialize as empty list
# rerun simulation so new include cells get recorded from
if rerun:
cellsRecord = [cell.gid for cell in sim.getCellsList(include)]
for cellRecord in cellsRecord:
if cellRecord not in sim.cfg.recordCells:
sim.cfg.recordCells.append(cellRecord)
sim.setupRecording()
sim.simulate()
colorList = [[0.42,0.67,0.84], [0.90,0.76,0.00], [0.42,0.83,0.59], [0.90,0.32,0.00],
[0.34,0.67,0.67], [0.90,0.59,0.00], [0.42,0.82,0.83], [1.00,0.85,0.00],
[0.33,0.67,0.47], [1.00,0.38,0.60], [0.57,0.67,0.33], [0.5,0.2,0.0],
[0.71,0.82,0.41], [0.0,0.2,0.5]]
tracesList = sim.cfg.recordTraces.keys()
tracesList.sort()
cells, cellGids, _ = getCellsInclude(include)
gidPops = {cell['gid']: cell['tags']['popLabel'] for cell in cells}
# time range
if timeRange is None:
timeRange = [0,sim.cfg.duration]
recordStep = sim.cfg.recordStep
figs = []
tracesData = []
# Plot one fig per cell
if oneFigPer == 'cell':
for gid in cellGids:
figs.append(figure()) # Open a new figure
fontsiz = 12
for itrace, trace in enumerate(tracesList):
if 'cell_'+str(gid) in sim.allSimData[trace]:
data = sim.allSimData[trace]['cell_'+str(gid)][int(timeRange[0]/recordStep):int(timeRange[1]/recordStep)]
t = arange(timeRange[0], timeRange[1]+recordStep, recordStep)
tracesData.append({'t': t, 'cell_'+str(gid)+'_'+trace: data})
color = colorList[itrace]
if not overlay:
subplot(len(tracesList),1,itrace+1)
color = 'blue'
plot(t[:len(data)], data, linewidth=1.5, color=color, label=trace)
xlabel('Time (ms)', fontsize=fontsiz)
ylabel(trace, fontsize=fontsiz)
xlim(timeRange)
if itrace==0: title('Cell %d, Pop %s '%(int(gid), gidPops[gid]))
if overlay:
maxLabelLen = 10
subplots_adjust(right=(0.9-0.012*maxLabelLen))
legend(fontsize=fontsiz, bbox_to_anchor=(1.04, 1), loc=2, borderaxespad=0.)
# Plot one fig per cell
elif oneFigPer == 'trace':
for itrace, trace in enumerate(tracesList):
figs.append(figure()) # Open a new figure
fontsiz = 12
for igid, gid in enumerate(cellGids):
if 'cell_'+str(gid) in sim.allSimData[trace]:
data = sim.allSimData[trace]['cell_'+str(gid)][int(timeRange[0]/recordStep):int(timeRange[1]/recordStep)]
t = arange(timeRange[0], timeRange[1]+recordStep, recordStep)
tracesData.append({'t': t, 'cell_'+str(gid)+'_'+trace: data})
color = colorList[igid]
if not overlay:
subplot(len(cellGids),1,igid+1)
color = 'blue'
ylabel(trace, fontsize=fontsiz)
plot(t[:len(data)], data, linewidth=1.5, color=color, label='Cell %d, Pop %s '%(int(gid), gidPops[gid]))
xlabel('Time (ms)', fontsize=fontsiz)
xlim(timeRange)
title('Cell %d, Pop %s '%(int(gid), gidPops[gid]))
if overlay:
maxLabelLen = 10
subplots_adjust(right=(0.9-0.012*maxLabelLen))
legend(fontsize=fontsiz, bbox_to_anchor=(1.04, 1), loc=2, borderaxespad=0.)
try:
tight_layout()
except:
pass
#save figure data
if saveData:
figData = {'tracesData': tracesData, 'include': include, 'timeRange': timeRange, 'oneFigPer': oneFigPer,
'saveData': saveData, 'saveFig': saveFig, 'showFig': showFig}
_saveFigData(figData, saveData, 'traces')
# save figure
if saveFig:
if isinstance(saveFig, str):
filename = saveFig
else:
filename = sim.cfg.filename+'_'+'traces.png'
savefig(filename)
# show fig
if showFig: _showFigure()
return figs