Added custom inputs and basic cluster analysis #1
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Test from Brian |
| @@ -1,40 +0,0 @@ | |||
| # Data Download | |||
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why did this file get deleted? undo undo!
| @@ -64,14 +65,14 @@ def adaptive_exp_net(all_param_dict): | |||
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| ### TO DO: also randomly initialize w to either randint(?)*b or randn*(v-v_rest)*a | |||
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| poisson_input_E = b2.PoissonInput( | |||
| ''' poisson_input_E = b2.PoissonInput( | |||
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what happened here? This func didn't need to be changed right (or is used at all)?
| @@ -64,14 +65,14 @@ def adaptive_exp_net(all_param_dict): | |||
| ) | |||
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| ### TO DO: also randomly initialize w to either randint(?)*b or randn*(v-v_rest)*a | |||
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| poisson_input_E = b2.PoissonInput( | |||
| ''' poisson_input_E = b2.PoissonInput( | |||
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what happened here? This func didn't need to be changed right (or is used at all)?
| @@ -64,14 +65,14 @@ def adaptive_exp_net(all_param_dict): | |||
| ) | |||
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| ### TO DO: also randomly initialize w to either randint(?)*b or randn*(v-v_rest)*a | |||
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| poisson_input_E = b2.PoissonInput( | |||
| ''' poisson_input_E = b2.PoissonInput( | |||
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what happened here? This func didn't need to be changed right (or is used at all)? The quotes are typos / accidents?
| @@ -64,14 +65,14 @@ def adaptive_exp_net(all_param_dict): | |||
| ) | |||
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| ### TO DO: also randomly initialize w to either randint(?)*b or randn*(v-v_rest)*a | |||
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| poisson_input_E = b2.PoissonInput( | |||
| ''' poisson_input_E = b2.PoissonInput( | |||
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what happened here? This func didn't need to be changed right (or is used at all)? The quotes are typos / accidents?
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Yes sorry I probably wanted to check if the custom inputs were working and silenced this to confirm, the Poisson input should be kept.
| @@ -17,6 +17,7 @@ | |||
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| def _filter_spikes_random(spike_trains, n_to_save): | |||
| """Filter a subset of spike trains randomly for saving.""" | |||
| np.random.seed(42) | |||
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I forgot if we talked about this but should this be reproduceably random, i.e., using the model random_seed?
| if n_to_save == len(spike_trains): | ||
| # recorded and to-be saved is the same length, go on a per usual | ||
| spike_dict[sm.name] = b2_interface._deunitize_spiketimes(spike_trains) | ||
| else: | ||
| # recorded more than necessary, subselect for saving | ||
| spike_dict[sm.name] = b2_interface._deunitize_spiketimes( | ||
| _filter_spikes_random(spike_trains, n_to_save) | ||
| _filter_spikes_random(spike_trains, n_to_save) # THIS IS WHERE THE NEURONS ARE RANDOMLY DROPPED BEFORE SAVING (AND PLOTTING??) |
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so it's not being randomly dropped anymore?
| @@ -674,3 +676,31 @@ def load_df_posteriors(path_dict): | |||
| path_dict["root_path"] + path_dict["params_dict_analysis_updated"] | |||
| ) | |||
| return df_posterior_sims, posterior, params_dict_default | |||
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| def sort_neurons(membership, sorting_method="cluster_identity"): | |||
| """ | |||
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nice this should be quite useful
| @@ -584,3 +583,126 @@ def plot_corr_pv(pvals, ax, alpha_level=0.05, fmt="w*", ms=0.5): | |||
| for j in range(pvals.shape[0]): | |||
| if pvals[i, j] < alpha_level: | |||
| ax.plot(j, i, fmt, ms=ms, alpha=1) | |||
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so this is not being used anymore because you extracted the sorting function right? Then I think it can be removed
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the two notebook files are nice and demonstrate the new capabilities well, but making it more like a demo / pedagogical notebook, with some more descriptions would be good, in the style of the two existing demo notebooks. I think some of the code can also be removed or at least cleaned up?
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