GSoC Example #39
GSoC Example #39
Conversation
Fitting multiple sets of parameters to the adaptive exponential IF model from Brette and Gerstner (2005). Example for GSoC project.
There was a problem hiding this comment.
Thanks for the example, looks very good to me in general. I made a few minor comments in the code, and it would be great to have a few more comments that explain how the three parameter regimes are handled (e.g. the shape of the list of lists, the duplicated parameter values in the beginning when you generate the ground truth data, etc.) – this might not be obvious to every user.
| metric = GammaFactor(delta=1*ms, time=140*ms) | ||
|
|
||
| fitters = [] | ||
| for i in range(len(out_spikes)): |
There was a problem hiding this comment.
This could be something like
for spikes in out_spikes:instead.
| #Put spike spikes and voltage traces into lists , probably lots of smarter ways to do this. | ||
| out_spikes = [[spike_train[0] / second, spike_train[1] /second], [spike_train[2] / second, spike_train[3] / second], [spike_train[4] / second, spike_train[5] / second]] | ||
| v_traces = [[trace.vm[0]/mV, trace.vm[1]/mV], [trace.vm[2]/mV, trace.vm[3]/mV], [trace.vm[4]/mV, trace.vm[5]/mV]] |
There was a problem hiding this comment.
I think it is ok as it is. There are "smarter" ways to do this, but they are also less clear. I'd probably change the formatting a bit, though. E.e. have spike_train[0], spike_train[1] on one line, and then spike_train[2], spike_train[3] on the next, etc.
Also, no need to divide by seconds here, and I'd rather keep the v_traces with the units as well (for more consistency in the plotting code).
| out_spikes = [[spike_train[0] / second, spike_train[1] /second], [spike_train[2] / second, spike_train[3] / second], [spike_train[4] / second, spike_train[5] / second]] | ||
| v_traces = [[trace.vm[0]/mV, trace.vm[1]/mV], [trace.vm[2]/mV, trace.vm[3]/mV], [trace.vm[4]/mV, trace.vm[5]/mV]] | ||
|
|
||
| start_scope() |
There was a problem hiding this comment.
This shouldn't be necessary here.
| ax[0, i].plot(trace.t/ms, v_traces[i][0], label='Simulated'); | ||
| ax[0, i].plot(trace.t/ms, fits[i][0]/mV, label='Fitted'); | ||
| ax[1, i].plot(trace.t/ms, v_traces[i][1]); | ||
| ax[1, i].plot(trace.t/ms, fits[i][1]/mV); |
| ax[0, 0].set_xlabel('Time (ms)') | ||
| ax[0, 0].set_ylabel('v (mV)') | ||
|
|
||
| plt.show() |
There was a problem hiding this comment.
Getting really nit-picky: please add a line break in the end :)
Fitting multiple sets of parameters to the adaptive exponential IF model from Brette and Gerstner (2005). Example for GSoC project.