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window.plotIV = function(protocolName, e){
e.preventDefault();
// figure out if we have any protocol and organize into a map
var experiments = Project.getExperiments();
var protocolExperimentsMap = {};
for(var i=0; i<experiments.length; i++){
if(experiments[i].getName().startsWith('[P]')){
// parse protocol pattern
var experimentName = experiments[i].getName();
var protocolName = experimentName.substring(experimentName.lastIndexOf("[P] ")+4,experimentName.lastIndexOf(" - "));
if(protocolExperimentsMap[protocolName] == undefined){
protocolExperimentsMap[protocolName] = [experiments[i]];
} else {
protocolExperimentsMap[protocolName].push(experiments[i]);
}
}
}
// look for experiments with that name
experiments = protocolExperimentsMap[protocolName];
var membranePotentials = GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith('.v');
var plotController = GEPPETTO.WidgetFactory.getController(GEPPETTO.Widgets.PLOT);
var plotWidget = null;
if(experiments.length > 0 && membranePotentials.length>0){
plotWidget = G.addWidget(0).setName(protocolName + ' / IV Curve').setSize(300, 500);
}
var if_results = {};
var iv_results = {};
for(var i=0; i<experiments.length; i++){
// loop and plot all membrane potentials
if(experiments[i].getStatus() == 'COMPLETED'){
for(var j=0; j<membranePotentials.length; j++){
plotController.plotStateVariable(
Project.getId(),
experiments[i].getId(),
membranePotentials[j],
plotWidget
);
}
}
}
for i in range(number_cells):
t = np.array(results['t'])*1000
v = np.array(results["%s[%i]/v"%(pop.id, i)])*1000
if plot_voltage_traces:
times_results.append(t)
volts_results.append(v)
volts_labels.append("%s nA"%stims[i])
var min = Math.min.apply(null, arr),
max = Math.max.apply(null, arr);
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm['maxima_times']
var freq = 0;
var count = 0;
if (spike_times.length > 2){
count = 0
}
for (var i =0;i<spike_times.length;i++){
if(spike_times[i]>=(pre_zero_pulse + analysis_delay) && (spike_times[i]< (pre_zero_pulse + analysis_duration+analysis_delay)){
count+=1;
freq = 1000 * count/float(analysis_duration);
}
}
var mean_freq = mean_spike_frequency(spike_times);
#print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if freq == 0:
if post_zero_pulse==0:
iv_results[stims[i]] = v[-1]
else:
v_end = None
for j in range(len(t)):
if v_end==None and t[j]>=end_stim:
v_end = v[j]
iv_results[stims[i]] = v_end
};
window.plotFI = function(protocolName, e){
};
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