jgrewe/gp_neurobio
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

buh

Browse Source
This commit is contained in:
efish 2018-11-30 10:00:00 +01:00
parent da80327826
commit 4d5110c4b9
5 changed files with 15 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
code/eod_chirp_beat.py
View File

@ -81,8 +81,8 @@ ax3.set_ylabel('EOD [mV]', fontsize=22)
ax3.xaxis.set_tick_params(labelsize=18) ax3.xaxis.set_tick_params(labelsize=18)
ax3.yaxis.set_tick_params(labelsize=18) ax3.yaxis.set_tick_params(labelsize=18)
ax3.set_xlabel('time [ms]', fontsize=22) ax3.set_xlabel('Time [ms]', fontsize=22)
ax4.set_xlabel('time [ms]', fontsize=22) ax4.set_xlabel('Time [ms]', fontsize=22)
ax4.xaxis.set_tick_params(labelsize=18) ax4.xaxis.set_tick_params(labelsize=18)
ax4.set_yticklabels([]) ax4.set_yticklabels([])

4
code/eod_freq_beat.py
View File

@ -28,9 +28,9 @@ fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
plt.plot(time[10000:20000]*1000, ampl, color='royalblue') plt.plot(time[10000:20000]*1000, ampl, color='royalblue')
plt.plot(time[10000:20000][p]*1000, ampl[p], lw=2, color='k') plt.plot(time[10000:20000][p]*1000, ampl[p], lw=2, color='k')
plt.plot(time[10000:20000][t]*1000, ampl[t], lw=2, color='k') plt.plot(time[10000:20000][t]*1000, ampl[t], lw=2, color='k')
ax.set_xlabel("time [ms]", fontsize = 22) ax.set_xlabel("Time [ms]", fontsize = 22)
plt.xticks(fontsize = 18) plt.xticks(fontsize = 18)
ax.set_ylabel("eod amplitude [mV]", fontsize = 22) ax.set_ylabel("EOD amplitude [mV]", fontsize = 22)
plt.yticks(fontsize = 18) plt.yticks(fontsize = 18)
ax.spines["top"].set_visible(False) ax.spines["top"].set_visible(False)
ax.spines["right"].set_visible(False) ax.spines["right"].set_visible(False)

11
code/plot_eodform_spikehist.py
View File

@ -26,7 +26,6 @@ eod_times = time[(eod_norm >= threshold) & (shift_eod < threshold)]
eod_duration = eod_times[2]- eod_times[1] #time in s eod_duration = eod_times[2]- eod_times[1] #time in s
eod_duration = eod_times[2]- eod_times[1]
@ -37,9 +36,9 @@ interspikeintervals = np.diff(spikes)/eod_duration
fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor)) fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
plt.hist(interspikeintervals, bins=np.arange(0, np.max(interspikeintervals), 0.1), color='royalblue') plt.hist(interspikeintervals, bins=np.arange(0, np.max(interspikeintervals), 0.1), color='royalblue')
plt.xlabel("eod cycles", fontsize = 22) plt.xlabel("EOD cycles", fontsize = 22)
plt.xticks(fontsize = 18) plt.xticks(fontsize = 18)
plt.ylabel("number of \n interspikeintervals", fontsize = 22) plt.ylabel("Number of \n interspikeintervals", fontsize = 22)
plt.yticks(fontsize = 18) plt.yticks(fontsize = 18)
ax.spines["top"].set_visible(False) ax.spines["top"].set_visible(False)
ax.spines["right"].set_visible(False) ax.spines["right"].set_visible(False)
@ -91,8 +90,8 @@ time_axis = np.arange(max_cut)/sampling_rate*1000
# plot eod form and spike histogram # plot eod form and spike histogram
fig, ax1 = plt.subplots(figsize=(20/inch_factor, 10/inch_factor)) fig, ax1 = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
ax1.hist(spike_times, color='firebrick') ax1.hist(spike_times, color='firebrick')
ax1.set_xlabel('time [ms]', fontsize=22) ax1.set_xlabel('Time [ms]', fontsize=22)
ax1.set_ylabel('number', fontsize=22) ax1.set_ylabel('Number', fontsize=22)
ax1.tick_params(axis='y', labelcolor='firebrick') ax1.tick_params(axis='y', labelcolor='firebrick')
plt.xticks(fontsize=18) plt.xticks(fontsize=18)
plt.yticks(fontsize=18) plt.yticks(fontsize=18)
@ -101,7 +100,7 @@ ax1.spines['top'].set_visible(False)
ax2 = ax1.twinx() ax2 = ax1.twinx()
ax2.fill_between(time_axis, mu_eod+std_eod, mu_eod-std_eod, color='royalblue', alpha=0.5) ax2.fill_between(time_axis, mu_eod+std_eod, mu_eod-std_eod, color='royalblue', alpha=0.5)
ax2.plot(time_axis, mu_eod, color='black', lw=2) ax2.plot(time_axis, mu_eod, color='black', lw=2)
ax2.set_ylabel('voltage [mV]', fontsize=22) ax2.set_ylabel('Voltage [mV]', fontsize=22)
ax2.tick_params(axis='y', labelcolor='royalblue') ax2.tick_params(axis='y', labelcolor='royalblue')
ax2.spines['top'].set_visible(False) ax2.spines['top'].set_visible(False)

8
code/repetition_firingrate.py
View File

@ -8,7 +8,7 @@ from IPython import embed
# define sampling rate and data path # define sampling rate and data path
sampling_rate = 40 #kHz sampling_rate = 40 #kHz
data_dir = "../data" data_dir = "../data"
dataset = "2018-11-09-ad-invivo-1" dataset = "2018-11-14-al-invivo-1"
inch_factor = 2.54 inch_factor = 2.54
# parameters for binning, smoothing and plotting # parameters for binning, smoothing and plotting
cut_window = 60 cut_window = 60
@ -88,14 +88,14 @@ for df in df_phase_time.keys():
ax[1].plot(time_axis[0+5*sampling_rate:-5*sampling_rate], smoothed_spikes[0+5*sampling_rate:-5*sampling_rate]*1000, color='royalblue', lw = 2) ax[1].plot(time_axis[0+5*sampling_rate:-5*sampling_rate], smoothed_spikes[0+5*sampling_rate:-5*sampling_rate]*1000, color='royalblue', lw = 2)
ax[0].set_title('$\Delta$f = %s Hz' %(df), fontsize = 18) ax[0].set_title('$\Delta$f = %s Hz' %(df), fontsize = 18)
ax[0].set_ylabel('repetition', fontsize=22) ax[0].set_ylabel('Repetition', fontsize=22)
ax[0].yaxis.set_label_coords(-0.1, 0.5) ax[0].yaxis.set_label_coords(-0.1, 0.5)
ax[0].set_yticks(np.arange(1, len(plot_trials)+1,2)) ax[0].set_yticks(np.arange(1, len(plot_trials)+1,2))
ax[0].set_yticklabels(np.arange(1, len(plot_trials)+1,2), fontsize=18) ax[0].set_yticklabels(np.arange(1, len(plot_trials)+1,2), fontsize=18)
ax[1].set_xlabel('time [ms]', fontsize=22) ax[1].set_xlabel('Time [ms]', fontsize=22)
ax[1].yaxis.set_label_coords(-0.1, 0.5) ax[1].yaxis.set_label_coords(-0.1, 0.5)
ax[1].set_ylabel('firing rate [Hz]', fontsize=22) ax[1].set_ylabel('Firing rate [Hz]', fontsize=22)
plt.xticks(fontsize=18) plt.xticks(fontsize=18)
plt.yticks(fontsize=18) plt.yticks(fontsize=18)
fig.tight_layout() fig.tight_layout()

4
code/stimulus_chirp.py
View File

@ -47,8 +47,8 @@ ax1.set_ylabel("field [mV]", fontsize = 22)
ax1.yaxis.set_label_coords(-0.1, 0.5) ax1.yaxis.set_label_coords(-0.1, 0.5)
ax2.set_xlabel("time [ms]", fontsize = 22) ax2.set_xlabel("Time [ms]", fontsize = 22)
ax2.set_ylabel("frequency [Hz]", fontsize = 22) ax2.set_ylabel("Frequency [Hz]", fontsize = 22)
ax2.yaxis.set_label_coords(-0.1, 0.5) ax2.yaxis.set_label_coords(-0.1, 0.5)
plt.xticks(fontsize=18) plt.xticks(fontsize=18)
plt.yticks(fontsize=18) plt.yticks(fontsize=18)