def figure_problems_noise_correlations_histogram(noise_type, noise_info, filename_format=None):
"""Savepath should be a string with {noise_type} to fill in a lowercase name of the noise"""
correlation_threshold = 0.05
correlation = noise_info['correlations']
title = noise_info['title']
ratio = sum(abs(correlation) <= correlation_threshold) / len(correlation)
print(f"Details about {noise_info['title']}:")
print(f"n = {len(correlation)}")
print(f"mean = {np.mean(correlation)}, var = {np.var(correlation)}")
print(f"{ratio * 100}% of the correlations are below the threshold of {correlation_threshold}")
num_bins = 400
stepwidth = 2 / num_bins
noise_histogram, bins = np.histogram(correlation, bins=num_bins, range=(-1, 1))
fig, ax = plt.subplots(figsize=(5.0, 3.8))
ax.bar(x=bins[:-1] + stepwidth, height=noise_histogram, width=stepwidth)
ax.set_xlabel('Correlation')
ax.set_ylabel('Count / 0.005')
# ax.set_title(title)
fig.show()
if filename_format:
filename = filename_format.format(noise_type=noise_type.lower())
plu.save_figure(fig, filename, noise_type=noise_type,
samples=len(correlation),
correlation_threshold=correlation_threshold,
below_threshold=ratio,
correlation_source="FigureMethodsNoiseCorrelations.m")
def figure_methods_injected_currents_frequency(runnumber, l2, filename_currents=None, filename_frequency=None):
### Define injected currents
num = 40
i_inh = np.linspace(0.4, 2.0, num)
i_exc = 0.4652 * i_inh ** 4 - 1.9860 * i_inh ** 3 + 3.2879 * i_inh ** 2 - 1.0623 * i_inh + 0.7546
xaxis = range(1, 41)
### Plot curves of injected currents:
fig_currents, ax = plt.subplots()
sns.lineplot(xaxis, i_exc, ax=ax, label=r'$I_{inj}^{exc}$', color='red')
sns.lineplot(xaxis, i_inh, ax=ax, label=r'$I_{inj}^{inh}$', color='blue')
ax.set_ylabel('Injected current (${\mu A / cm^2}$)')
ax.set_xlabel("Index of injected currents")
# ax.set_title("Injected currents $I_{inj}^{inh}$ and $I_{inj}^{exc}$")
fig_currents.show()
plu.save_figure(fig_currents, filename_currents, runnumbers=[runnumber], l2=l2)
# if savefigures:
# fig_currents.savefig(os.path.join(settings.py_figures_dir, f'figure_injected_currents_exc_inh.png'), bbox_inches='tight', pad_inches=0.1)
### Get frequency and PPC curve of runnumber
analysis_standard_df_reg1, analysis_standard_df_reg2 = mlu.run_analysis_standard_to_df(runnumber=runnumber)
freqe = analysis_standard_df_reg1['freqe'].loc[:, l2]
avgmorfreq = analysis_standard_df_reg1['avgmorfreq'].loc[:, l2]
phaselocke = analysis_standard_df_reg1['Phaselocke'].loc[:, l2]
### Plot curves of frequency and PPC (Phaselock)
fig_frequency, ax_freq = plt.subplots()
ax_phaselock = ax_freq.twinx()
# ax_phaselock.axhline(y=0.1, color='black', alpha=0.9, linestyle='--') # Threshold line for extremely low PPC (i.e., no real oscillations)
sns.lineplot(y=phaselocke, x=xaxis, ax=ax_phaselock, label='PPC value', color='black')
ax_phaselock.set_ylim([0, 0.8])
ax_phaselock.set_ylabel("PPC value")
sns.lineplot(y=avgmorfreq, x=xaxis, ax=ax_freq, label='Frequency (Morlet)')
sns.lineplot(y=freqe, x=xaxis, ax=ax_freq, label='Frequency (Autocorrelation)')
# ax_freq.set_xticklabels(np.linspace(1, 40, 41))
ax_freq.set_xlim(left=0, right=41)
ax_freq.set_xlabel("Index of injected currents")
ax_freq.set_ylim([35, 75])
ax_freq.set_ylabel("Frequency (Hz)")
ax_freq.legend(loc='upper left')
# ax_freq.set_title("Intrinsic frequency and PPC")
fig_frequency.show()
plu.save_figure(fig_frequency, filename_frequency, runnumbers=[runnumber], l2=l2)
def figure_results_correlation_boxplots_compare_thresholds(
runnumbers_sett, filename_format, analysis_info2_name,
compare_thresholds):
"""
:param runnumbers_sett:
:param filename_format: Needs {analysis_info2_name}!
:param analysis_info2_name:
:param compare_thresholds:
:return:
"""
corr_df2 = __figure_results_correlation_boxplots_prepare_df(
runnumbers_sett)
fig, ax = plt.subplots(ncols=2, sharey=True, figsize=figsize)
for i, threshold in enumerate(compare_thresholds):
sns.violinplot(x='feedback',
y=analysis_info2_name,
hue='Noiseseed',
split=True,
data=corr_df2[corr_df2['coh'] >= threshold],
ax=ax[i],
scale='count',
inner='box',
cut=0,
linewidth=1.5)
if threshold == 0:
ax[i].set_title("All conditions")
pass
else:
ax[i].set_title(f"Threshold $\geq$ {threshold}")
pass
ax[i].set_xlabel(r"Feedback $g_{{2 \to 1}}^{{e \to i}}$ in $mS/cm^2$")
# fig.suptitle(mlu.derive_analysis_info2_title(analysis_info2_name))
ax[0].set_ybound(None, 1)
ax[0].set_ylabel('Correlation')
ax[0].get_legend().remove()
fig.show()
if filename_format:
filename = filename_format.format(
analysis_info2_name=analysis_info2_name)
plu.save_figure(fig, filename=filename, runnumbers=runnumbers_sett)
def plot_3_ts(dates,
data_1,
data_2,
data_3,
x_label,
y1_label,
y2_label,
y3_label,
title,
save=False):
fig, axarr = plt.subplots(3, sharex=True, sharey=False)
axarr[0].plot(dates, data_1)
axarr[1].plot(dates, data_2)
axarr[2].plot(dates, data_3)
axarr[0].set_ylabel(y1_label)
axarr[1].set_ylabel(y2_label)
axarr[2].set_ylabel(y3_label)
axarr[2].set_title(title, y=-0.75, fontsize=16)
if save: pu.save_figure(plt, title, 'compare', lgd=None)
def figure_results_correlation_boxplots_compare_signals(
runnumbers_sett, filename_format, compare_signals):
"""
:param filename_format: Needs {compare_signal0} and {compare_signal1}!
:param runnumbers_sett:
:param compare_signals:
:return:
"""
corr_df2 = __figure_results_correlation_boxplots_prepare_df(
runnumbers_sett)
fig, ax = plt.subplots(ncols=2, sharey=True, figsize=figsize)
for i, analysis_info2_name in enumerate(compare_signals):
means = corr_df2.groupby(['feedback', 'Noiseseed'],
as_index=False).mean()[analysis_info2_name]
print(means)
sns.violinplot(x='feedback',
y=analysis_info2_name,
hue='Noiseseed',
split=True,
data=corr_df2,
ax=ax[i],
scale='count',
inner='box',
cut=0,
linewidth=1.5)
ax[i].set_ylabel('')
ax[i].set_title(mlu.derive_analysis_info2_title(analysis_info2_name))
ax[i].set_xlabel(r"Feedback $g_{{2 \to 1}}^{{e \to i}}$ in $mS/cm^2$")
ax[0].set_ybound(None, 1.1)
ax[0].set_ylabel('Correlation')
ax[0].get_legend().remove()
fig.show()
if filename_format:
filename = filename_format.format(compare_signal0=compare_signals[0],
compare_signal1=compare_signals[1])
plu.save_figure(fig, filename=filename, runnumbers=runnumbers_sett)
def methods_coherence_slepian_sequences(T, TW, filename=None):
# Generate the slepian sequences, here using the time-halfbandwith-product
[w, eigens] = spectrum.dpss(T, TW / 2, 4)
# fig, ax = plt.subplots(figsize=(8, 5))
fig, ax = plt.subplots(figsize=(6, 4.4))
# ax.canvas(200, 350)
sns.lineplot(data=w, ax=ax)
ax.set_xlim([100, 900])
ax.set_xlabel(r"Time t in $ms$")
ax.set_ylim([-0.12, 0.12])
ax.legend(['1st sequence', '2nd sequence', '3rd sequence', '4th sequence'])
# ax.set_title(f"Slepian sequences for T={T}, TW={TW}")
fig.show()
plu.save_figure(fig, filename, T=T, TW=TW)
def figure_problemns_noise_compare(noise_type, filename_format):
"""
Savepath should be a string with {noise_type} to fill a lowercase name of the noise in
:param savepath:
:return:
"""
noise_examples = mlu.loadmat('./mat/noise_examples.mat')
Fs = 20 # Sampling rate: samples/millisecond
T = 1000 # plot T seconds of noise
noise_example = noise_examples[noise_type]
n = len(noise_example) # Number of points
x = np.linspace(0, T, T*Fs)
fig, ax = plt.subplots()
for region in [0, 1]:
y = noise_example[region][0:T * Fs]
sns.lineplot(x, y, ax=ax, label=f"Noise to region {region+1}")
ax.set_ylim([-1.2, 1.2])
ax.legend(loc='upper left')
# ax.set_title(f"{noise_type} noise")
ax.set_xlabel("Time t in $ms$")
ax.set_ylabel("$I_{noise}$ in $\mu A/cm^2$")
fig.show()
if filename_format:
filename = filename_format.format(noise_type=noise_type.lower())
plu.save_figure(fig, filename, noise_type=noise_type, source='FigureMethodsNoiseExamples.m')
def methods_analysis_spike_density_histogram(runnumber,
l1,
l2,
region,
start,
stop,
filename=None):
sett = mlu.get_clean_settings(runnumber)['sett']
spikes_excitatory, spikes_inhibitory = mlu.get_spiketrains_df(
runnumber, l1, l2)
spikes_excitatory[
'neuron_idx'] = spikes_excitatory['neuron_idx'] + sett['Ni']
# Filter for region
spikes_excitatory = spikes_excitatory[spikes_excitatory['region'] ==
region]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['region'] ==
region]
# Filter for start <= t <= end
spikes_excitatory = spikes_excitatory[spikes_excitatory['t'] >= start]
spikes_excitatory = spikes_excitatory[spikes_excitatory['t'] <= stop]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['t'] >= start]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['t'] <= stop]
# Bin the spikes for histograms
bins = np.linspace(start=start,
stop=stop,
num=int((stop - start) / sett['dthist'] + 1),
endpoint=True)
excitatory_spikes_binned, _ = np.histogram(spikes_excitatory['t'],
bins=bins)
inhibitory_spikes_binned, _ = np.histogram(spikes_inhibitory['t'],
bins=bins)
excitatory_spikes_density = 1000 * 1 / (
sett['dthist'] * sett['Ne']) * excitatory_spikes_binned
inhibitory_spikes_density = 1000 * 1 / (
sett['dthist'] * sett['Ni']) * inhibitory_spikes_binned
fig, ax = plt.subplots(nrows=2, sharex=True, figsize=(10, 4.5))
ax[0].bar(x=bins[:-1],
height=excitatory_spikes_density,
color='red',
label='Pyramidal cells')
ax[1].bar(x=bins[:-1],
height=inhibitory_spikes_density,
color='blue',
label='Interneurons')
handles = [
mpatches.Patch(color='red', label='Pyramidal cells'),
mpatches.Patch(color='blue', label='Interneurons')
]
ax[0].legend(handles=handles, loc='upper right')
ax[1].invert_yaxis()
fig.subplots_adjust(wspace=0, hspace=0)
ax[1].set_xlabel('Time t ($ms$)')
ax[0].set_ylabel('Spikes/s')
ax[1].set_ylabel('Spikes/s')
# ax[0].set_title(
# f"Pyramidal cell (upper) and interneuron (lower) spike density plots")
fig.show()
ppc_value = mlu.run_analysis_standard_to_df(runnumber)[
region - 1]['Phaselocke'][l1 - 1, l2 - 1]
plu.save_figure(fig,
filename,
runnumbers=[runnumber],
l1=l1,
l2=l2,
region=region,
start=start,
stop=stop,
ppc_value=ppc_value)
def methods_analysis_spikes_scatterplot(runnumber,
l1,
l2,
region,
start,
stop,
filename=None):
sett = mlu.get_clean_settings(runnumber)['sett']
spikes_excitatory, spikes_inhibitory = mlu.get_spiketrains_df(
runnumber, l1, l2)
spikes_excitatory[
'neuron_idx'] = spikes_excitatory['neuron_idx'] + sett['Ni']
# Filter for region
spikes_excitatory = spikes_excitatory[spikes_excitatory['region'] ==
region]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['region'] ==
region]
# Filter for start <= t <= end
spikes_excitatory = spikes_excitatory[spikes_excitatory['t'] >= start]
spikes_excitatory = spikes_excitatory[spikes_excitatory['t'] <= stop]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['t'] >= start]
spikes_inhibitory = spikes_inhibitory[spikes_inhibitory['t'] <= stop]
# Plot spikes in scatterplot
fig, ax = plt.subplots(figsize=(10, 4))
sns.scatterplot(x='t',
y='neuron_idx',
color='red',
s=6,
data=spikes_excitatory,
ax=ax,
label='Pyramidal Cells')
sns.scatterplot(x='t',
y='neuron_idx',
color='blue',
s=6,
data=spikes_inhibitory,
ax=ax,
label='Interneurons')
ax.set_ylim(ymin=-20)
ax.set_ylabel('Neuron index')
ax.set_xlabel('Time t ($ms$)')
ax.legend(loc='upper left')
# ax.set_title('Pyramidal cell (red) and interneuron (blue) spiketrains')
# Create dummy Line2D objects for legend
h1 = Line2D([0], [0],
marker='o',
markersize=np.sqrt(30),
color='red',
linestyle='None')
h2 = Line2D([0], [0],
marker='o',
markersize=np.sqrt(30),
color='blue',
linestyle='None')
ax.legend([h1, h2], ['Pyramidal cells', 'Interneurons'], loc='upper right')
fig.show()
ppc_value = mlu.run_analysis_standard_to_df(runnumber)[
region - 1]['Phaselocke'][l1 - 1, l2 - 1]
print('ppc_value: ', ppc_value)
plu.save_figure(fig,
filename,
runnumbers=[runnumber],
l1=l1,
l2=l2,
region=region,
start=start,
stop=stop,
ppc_value=ppc_value)
def figure_problems_noise_to_region_correlation_vs_frequency(
region_to, filename=None):
noise_types = {
'brown10': {
'runnumbers': [117, 118, 122],
'title': "Strong Brown noise",
'color': '#572b0c', # Saddle Brown
'style': '-',
},
'brown05': {
'runnumbers': [140, 134, 141],
'title': "Weak Brown noise",
'color': '#9c4e15', # Saddle Brown
'style': '--',
},
'pink': {
'runnumbers': [112, 115, 114],
'title': "Pink noise",
'color': '#FF1493', # Deep Pink
'style': '-.'
},
'white': {
'runnumbers': [123, 156, 157],
'title': "White noise",
'color': '#808080', # Web Gray
'style': ':'
},
}
analysis_info2_name = f'rhos_fper_noise1_reg{region_to}'
# analysis_info2_lag = f'{analysis_info2_name}_lag0'
method = mlu.METHOD_CORRELATION_MAX
fig, ax = plt.subplots()
for noise_type, noise_details in noise_types.items():
runnumbers = noise_details['runnumbers']
correlation_dfs = [
mlu.get_run_correlations(
runnumber, method, [analysis_info2_name])[analysis_info2_name]
for runnumber in runnumbers
]
correlation_mean_line = pd.concat(correlation_dfs).groupby(
level=[0]).mean()
print(f"Details about {noise_details['title']}:")
print(f"Mean {np.mean(correlation_mean_line)}")
noise_details['correlation_mean'] = np.mean(correlation_mean_line)
ax.plot(correlation_mean_line,
color=noise_details['color'],
label=noise_details['title'],
linestyle=noise_details['style'])
ax.set_xlabel("Intrinsic frequency of region 1 ($Hz$)")
ax.set_xticks(np.linspace(0, 39, 7))
xticklabels = np.linspace(35, 65, 7)
ax.set_xticklabels(xticklabels)
ax.set_ylabel("Correlation")
ax.set_ylim(-0.08, 1.02)
# ax.set_title(f"Mean correlation between noise$_1$ and firing rate of region {region_to}")
ax.legend(loc='upper right', bbox_to_anchor=(1, 0.92))
fig.show()
plu.save_figure(fig,
filename,
region_to=region_to,
noise_types=noise_types)
def figure_results_feedforward_conductance_frequency(runnumber, l1,
filename_format):
"""
Plots the change in region 2 frequency in dependence on the total synaptic conductance from region 1 to region 2
:param runnumber:
:param l1:
:param filename_format:
:return:
"""
sett = mlu.get_clean_settings(runnumber)['sett']
feedback_conductance_ei = sett['g_syn_ei_r'][0, 1]
run_settings_loops = mlu.get_run_loops(runnumber)
analysis_standard_reg1_df, analysis_standard_reg2_df = mlu.run_analysis_standard_to_df(
runnumber)
avgmorfreqs1 = analysis_standard_reg1_df['avgmorfreq'][l1]
avgmorfreqs2 = analysis_standard_reg2_df['avgmorfreq'][l1]
i_inj_exc = run_settings_loops[1]['values_excitatory'][l1].round(2)
i_inj_inh = run_settings_loops[1]['values_inhibitory'][l1].round(2)
synaptic_conductances = run_settings_loops[2]['values'].round(2)
print(f"Frequency of region 1: {avgmorfreqs1[0]}")
print(f"Starting frequency of region 2: {avgmorfreqs2[0]}")
print(f"Ending frequency of region 2: {list(avgmorfreqs2)[-1]}")
fig, ax = plt.subplots(figsize=(6.4, 4.4))
sns.scatterplot(x=synaptic_conductances,
y=avgmorfreqs1,
s=30,
ax=ax,
label="Region 1")
sns.scatterplot(x=synaptic_conductances,
y=avgmorfreqs2,
s=30,
ax=ax,
label="Region 2")
ax.set_xlabel(
r"Total synaptic conductance $g_{1 \to 2}^{e \to e, i}$ ($mS/cm^2$)")
ax.set_ylim([39, 71])
ax.set_ylabel('Frequency ($Hz$)')
# ax.set_title(f"Frequency modulation through synaptic conductance")
ax.legend(loc='upper left')
if feedback_conductance_ei != 0:
text = mlu.get_infobox_text(
feedback_conductance_ee=None,
feedback_conductance_ei=feedback_conductance_ei)
# text = f"$reg_{2}^{{exc}} \\rightarrow reg_{1}^{{inh}}={feedback_conductance_ei} mS/cm^2$"
plu.set_textbox(ax, text, loc='upper right')
fig.show()
if filename_format:
filename = filename_format.format(runnumber=runnumber, l1=l1)
plu.save_figure(fig,
filename,
runnumbers=[runnumber],
l1=l1,
i_inj_exc=i_inj_exc,
i_inj_inh=i_inj_inh,
reg1_freq=avgmorfreqs1[0],
reg2_freq_start=avgmorfreqs2[0],
reg2_freq_end=list(avgmorfreqs2)[-1])
def figure_appendix_analysis_standard_heatmap_with_feedback(
runnumbers,
region,
analysis_standard_name,
filename_format,
debug=False):
"""
:param runnumbers: All runnumbers need to have the same settings except seed!
:param filename: needs {analysis_standard_name} {feedback_conductance_ee} and {feedback_conductance_ei} and {region}
:return:
"""
sett = mlu.get_clean_settings(runnumbers[0])['sett']
feedback_conductance_ee = sett['g_syn_ee_r'][0, 1]
feedback_conductance_ei = sett['g_syn_ei_r'][0, 1]
# Compute the means for standard analyses
analyses_standard = {}
group_analyses_standard_reg = [
mlu.run_analysis_standard_to_df(runnumber)[region]
for runnumber in runnumbers
]
analyses_standard[region] = pd.concat(group_analyses_standard_reg).groupby(
level=[0, 1]).mean()
# # Compute the mean over all runnumbers for standard2 analysis
# analyses_standard2_dfs = [mlu.run_analysis_standard2_to_df(runnumber) for runnumber in runnumbers]
# analysis_standard2_mean = pd.concat(analyses_standard2_dfs).groupby(level=[0, 1]).mean()
if analysis_standard_name in ['Phaselocke', 'Phaselocki']:
vmin = 0
vmax = 1
elif analysis_standard_name in [
'freqe', 'freqi', 'avgmorfreq', 'avgmorfreqi'
]:
vmin = 35
vmax = 80
elif analysis_standard_name in ['re', 'ri']:
vmin = 10
vmax = 100
else:
vmin = None
vmax = None
## Plotting coherence
fig, ax = plt.subplots()
sns.heatmap(analyses_standard[region]
[analysis_standard_name].unstack().transpose(),
ax=ax,
vmin=vmin,
vmax=vmax,
cmap='inferno')
ax.invert_yaxis()
plu.set_heatmap_axes(ax)
analysis_title = mlu.analysis_standard_names[
analysis_standard_name] if not mlu.analysis_standard_names[
analysis_standard_name] == "" else analysis_standard_name
ax.set_title(f'{analysis_title} of region {region+1}')
text = mlu.get_infobox_text(
feedback_conductance_ei=feedback_conductance_ei,
feedback_conductance_ee=feedback_conductance_ee,
runnumbers=runnumbers,
debug=debug,
show_info_fb_inh=True)
plu.set_textbox(ax, text)
fig.show()
if filename_format:
# Convert the float into a string. We are always <1, so cut off everything in front of decimal
feedback_conductance_ee_str = "{:4.3f}".format(
feedback_conductance_ee).replace(".", "_")[2:]
feedback_conductance_ei_str = "{:4.3f}".format(
feedback_conductance_ei).replace(".", "_")[2:]
filename = filename_format.format(
feedback_conductance_ee=feedback_conductance_ee_str,
feedback_conductance_ei=feedback_conductance_ei_str,
region=region,
analysis_standard_name=analysis_standard_name.lower())
plu.save_figure(fig,
filename,
runnumbers=runnumbers,
feedback_conductance_ee=feedback_conductance_ee,
feedback_conductance_ei=feedback_conductance_ei)
def figure_results_correlation_heatmap(runnumbers,
analysis_info2_name,
coherence_threshold,
filename_format,
debug=False,
show_info_fb_inh=True):
analysis_info2_title = mlu.derive_analysis_info2_title(analysis_info2_name)
sett = mlu.get_clean_settings(runnumbers[0])['sett']
feedback_conductance_ee = sett['g_syn_ee_r'][0, 1]
feedback_conductance_ei = sett['g_syn_ei_r'][0, 1]
noise_title = mlu.get_noise_title(sett['noiseamp'], sett['noisetype'])
analysis_standard2_df = mlu.run_analysis_standard2_to_df(runnumbers[0])
coherences_all = [
mlu.run_analysis_standard2_to_df(runnumber) for runnumber in runnumbers
]
coherences = pd.concat(coherences_all).groupby(level=[0, 1]).mean()['coh']
# print(analysis_standard2_df[analysis_standard2_df['coh'] >= coherence_threshold])
correlations_all = [
mlu.get_max_correlations(runnumber) for runnumber in runnumbers
]
correlations = pd.concat(correlations_all).groupby(level=[0, 1]).mean()
correlations = correlations[analysis_info2_name]
correlations[coherences < coherence_threshold] = np.nan
print(
f"{analysis_info2_name}, feedback {feedback_conductance_ei} mS/cm^2. Correlation limits (min, max): ({correlations.min()},{correlations.max()})"
)
fig, ax = plt.subplots()
sns.heatmap(correlations.unstack().transpose(),
cmap='coolwarm',
vmin=-0.3,
vmax=1,
center=0,
ax=ax)
ax.invert_yaxis()
plu.set_heatmap_axes(ax)
# Insert a textbox listing the feedback conductance
text = mlu.get_infobox_text(
feedback_conductance_ee=feedback_conductance_ee,
feedback_conductance_ei=feedback_conductance_ei,
runnumbers=runnumbers,
debug=debug,
show_info_fb_inh=True)
plu.set_textbox(ax, text, loc='lower right')
# ax.set_title(f"{analysis_info2_title}")
ax.legend(loc='lower right')
fig.show()
if filename_format:
# Convert the float into a string. We are always <1, so cut off everything in front of decimal
feedback_conductance_ee_str = "{:4.3f}".format(
feedback_conductance_ee).replace(".", "_")[2:]
feedback_conductance_ei_str = "{:4.3f}".format(
feedback_conductance_ei).replace(".", "_")[2:]
coherence_threshold_str = "{:3.2f}".format(
coherence_threshold).replace('.', "")
filename = filename_format.format(
analysis_info2_name=analysis_info2_name,
feedback_conductance_ee=feedback_conductance_ee_str,
feedback_conductance_ei=feedback_conductance_ei_str,
coherence_threshold=coherence_threshold_str)
plu.save_figure(fig,
filename,
runnumbers=runnumbers,
feedback_conductance_ee=feedback_conductance_ee,
feedback_conductance_ei=feedback_conductance_ei,
analysis_info2_name=analysis_info2_name,
coherence_threshold=coherence_threshold)
def figure_results_lag_vs_correlation_lines(runnumber, signal_type, signal_from, region_from, region_to,
coherence_threshold, filename_format=None):
if region_from == region_to:
coherence_threshold = 0
coherences = mlu.run_analysis_standard2_to_df(runnumber)['coh']
correlations, lags = mlu.run_analysis_info2_to_df(runnumber)
analysis_info2_name = f'rhos_{signal_type}_{signal_from}{region_from}_reg{region_to}'
correlations = correlations[analysis_info2_name][coherences >= coherence_threshold]
maximum_correlations_lags = []
min_lag = -35
max_lag = 30 # in ms
title = mlu.derive_analysis_info2_title(analysis_info2_name)
fig, ax = plt.subplots(figsize=(10, 5))
for index_condition in correlations.unstack(2).index:
condition_correlations = correlations.loc[index_condition]
condition_lags = lags
sns.lineplot(x=condition_lags, y=condition_correlations, zorder=10)
#### Filtering:
condition_correlations[condition_lags > mlu.CORRELATION_TMAX] = 0
condition_correlations[condition_lags < mlu.CORRELATION_TMIN] = 0
condition_idx_of_max_correlation = condition_correlations.idxmax()
filtered_lag = condition_lags[condition_idx_of_max_correlation]
maximum_correlations_lags.append(filtered_lag)
maximum_correlation_histogram, _ = np.histogram(maximum_correlations_lags, bins=lags)
ax.axvline(mlu.CORRELATION_TMIN, linestyle='--', c='grey')
ax.axvline(mlu.CORRELATION_TMAX, linestyle='--', c='grey')
ax.set_xlim([mlu.CORRELATION_TMIN - 5, mlu.CORRELATION_TMAX + 5])
ax.set_xlabel('Lag $\Delta t$ in ms')
ax.set_ylabel('Correlation')
ax.set_ylim([-0.1, 1])
ax2 = ax.twinx()
ax2.bar(x=lags[:-1], height=maximum_correlation_histogram, width=0.5, zorder=1, alpha=0.6)
# ax2.set_yticks(np.arange(0, max(maximum_correlation_histogram)+1), 5)
ax2.set_ylabel("Count")
# ax.set_title(
# f'{title} vs Lag')
fig.show()
if filename_format:
filename = filename_format.format(runnumber=runnumber, analysis_info2_name=analysis_info2_name)
plu.save_figure(fig, filename, analysis_info2_name=analysis_info2_name, coherence_threshold=coherence_threshold)
def figure_results_coherence_heatmap_with_feedback(runnumbers,
filename_format,
show_info_fb_inh=True,
debug=False):
"""
:param runnumbers: All runnumbers need to have the same settings except seed!
:param filename: needs {feedback_conductance_ee} and {feedback_conductance_ei}
:return:
"""
sett = mlu.get_clean_settings(runnumbers[0])['sett']
feedback_conductance_ee = sett['g_syn_ee_r'][0, 1]
feedback_conductance_ei = sett['g_syn_ei_r'][0, 1]
# Compute the mean over all runnumbers for standard2 analysis
analyses_standard2_dfs = [
mlu.run_analysis_standard2_to_df(runnumber) for runnumber in runnumbers
]
analysis_standard2_mean = pd.concat(analyses_standard2_dfs).groupby(
level=[0, 1]).mean()
coherence_mean = analysis_standard2_mean['coh']
print(
f"Runs {runnumbers} coherence >= {coherence_threshold}: {sum(coherence_mean >= coherence_threshold)}"
)
## Plotting coherence
fig, ax = plt.subplots()
sns.heatmap(coherence_mean.unstack().transpose(),
cmap='inferno',
ax=ax,
vmin=0,
vmax=1)
ax.invert_yaxis()
plu.set_heatmap_axes(ax)
# ax.set_title(f'Coherence - pyramidal neurons')
# Insert a textbox listing the feedback conductance
text = mlu.get_infobox_text(
feedback_conductance_ee=feedback_conductance_ee,
feedback_conductance_ei=feedback_conductance_ei,
debug=debug,
show_info_fb_inh=show_info_fb_inh)
plu.set_textbox(ax, text)
fig.show()
if filename_format:
# Convert the float into a string. We are always <1, so cut off everything in front of decimal
feedback_conductance_ee_str = "{:4.3f}".format(
feedback_conductance_ee).replace(".", "_")[2:]
feedback_conductance_ei_str = "{:4.3f}".format(
feedback_conductance_ei).replace(".", "_")[2:]
filename = filename_format.format(
feedback_conductance_ee=feedback_conductance_ee_str,
feedback_conductance_ei=feedback_conductance_ei_str)
plu.save_figure(fig,
filename,
runnumbers=runnumbers,
feedback_conductance_ee=feedback_conductance_ee,
feedback_conductance_ei=feedback_conductance_ei)
def figure_problems_shifting_windows_noise_signal(runnumber, l1, l2, run_frequency, data_source, filename):
noise_signal_dataset = mlu.loadmat(data_source)
dthist = 0.5
t_start = 0
t_stop = 500
noise_shift = int(1000 / (run_frequency * dthist))
idx_stop = int(t_stop / dthist) + noise_shift
sig_noise = noise_signal_dataset['sig_noise']
sig_fper = noise_signal_dataset['sigfper']
sig_freq = noise_signal_dataset['sigfreq']
sig_noise1_norm = norm_signal(sig_noise[0, :idx_stop])
sig_fper1_norm = norm_signal(sig_fper[:idx_stop, 0])
sig_fper2_norm = norm_signal(sig_fper[:idx_stop, 1])
sig_freq1_norm = norm_signal(sig_freq[:idx_stop, 0])
sig_freq2_norm = norm_signal(sig_freq[:idx_stop, 1])
n = len(sig_noise1_norm) - noise_shift
t = n * dthist # in ms
x = np.linspace(0, t, n)
factor = 3.5/6.5
width = 8
height = 8*factor
fig, ax = plt.subplots(figsize=(10, 4.4))
ax.plot(x, sig_noise1_norm[noise_shift:], color='#9c4e15', label=r'$\rm{Noise}_1$')
ax.plot(x, sig_fper1_norm[noise_shift:], label='Region 1 Firing rate')
ax.plot(x, sig_fper1_norm[:-noise_shift], label='Region 1 Firing rate after shift')
# ax.plot(x, sig_freq1_norm[noise_shift:], label='Region 1 Frequency')
# ax.plot(x, sig_fper2_norm[noise_shift:], label='Region 2 Firing rate')
# ax.plot(x, sig_freq2_norm[noise_shift:], label='Region 2 Frequency')
for arrow_x in [50, 170, 234, 330, 433]:
# arrow_x = (200)
arrow_y = sig_fper1_norm[int(arrow_x / dthist) + noise_shift]
arrow_dx = noise_shift * dthist - 1
arrow_dy = 0
ax.arrow(arrow_x, arrow_y, arrow_dx, arrow_dy, head_width=0.015, head_length=5, length_includes_head=True,
fc='black')
# ax.plot(x, sig_freq1_norm[noise_shift:], label='Region 1 Frequency before shift')
# ax.plot(x, sig_freq1_norm[:-noise_shift], label='Region 1 Frequency')
# ax.plot(x, sig_fper2_norm[:-noise_shift], label='Region 2 Firing rate')
ax.legend(loc='upper right')
ax.set_xlim(t_start, t_stop)
ax.set_xlabel("Time t ($ms$)")
ax.set_ylim(-0.1, 1.05)
ax.set_yticks([])
ax.set_yticklabels([])
# ax.set_title("Noise and region signals after shift")
fig.show()
print(f"Frequency of the circuit: {run_frequency} Hz")
plu.save_figure(fig, filename, runnumbers=[runnumber], l1=l1, l2=l2, run_frequency=run_frequency,
data_source=data_source)
def plot_array(dates, array, title, save=False):
plt.figure()
for plot_item in array:
plt.plot(dates, plot_item)
plt.title(title, fontsize=16)
if save: pu.save_figure(plt, title, 'array', lgd=None)