From ebd8e5ee255b92500ab490230627ffb4d3ccc411 Mon Sep 17 00:00:00 2001 From: efish Date: Thu, 29 Nov 2018 17:15:51 +0100 Subject: [PATCH 1/4] buh --- code/eod_freq_beat.py | 10 +++++----- code/repetition_firingrate.py | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/code/eod_freq_beat.py b/code/eod_freq_beat.py index 04ed6e7..71e42cc 100644 --- a/code/eod_freq_beat.py +++ b/code/eod_freq_beat.py @@ -25,9 +25,9 @@ time_axis = np.arange(len(ampl)) fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor)) -plt.plot(time[10000:20000], ampl) -plt.plot(time[10000:20000][p], ampl[p], lw=2, color='k') -plt.plot(time[10000:20000][t], ampl[t], lw=2, color='k') +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][t]*1000, ampl[t], lw=2, color='k') ax.set_xlabel("time [ms]", fontsize = 22) plt.xticks(fontsize = 18) ax.set_ylabel("eod amplitude [mV]", fontsize = 22) @@ -36,8 +36,8 @@ ax.spines["top"].set_visible(False) ax.spines["right"].set_visible(False) fig.tight_layout() -plt.show() -#plt.savefig('beat.png') +#plt.show() +plt.savefig('beat.png') diff --git a/code/repetition_firingrate.py b/code/repetition_firingrate.py index 1047b45..30d8b41 100644 --- a/code/repetition_firingrate.py +++ b/code/repetition_firingrate.py @@ -8,7 +8,7 @@ from IPython import embed # define sampling rate and data path sampling_rate = 40 #kHz data_dir = "../data" -dataset = "2018-11-14-al-invivo-1" +dataset = "2018-11-09-ad-invivo-1" inch_factor = 2.54 # parameters for binning, smoothing and plotting cut_window = 60 @@ -87,7 +87,7 @@ 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[0].set_title('df = %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].yaxis.set_label_coords(-0.1, 0.5) ax[0].set_yticks(np.arange(1, len(plot_trials)+1,2)) From da80327826b961279ec6da317f7e6724e26bd25e Mon Sep 17 00:00:00 2001 From: efish Date: Fri, 30 Nov 2018 09:07:44 +0100 Subject: [PATCH 2/4] buh --- code/stimulus_chirp.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/code/stimulus_chirp.py b/code/stimulus_chirp.py index 0e01894..4558c3d 100644 --- a/code/stimulus_chirp.py +++ b/code/stimulus_chirp.py @@ -52,6 +52,10 @@ ax2.set_ylabel("frequency [Hz]", fontsize = 22) ax2.yaxis.set_label_coords(-0.1, 0.5) plt.xticks(fontsize=18) plt.yticks(fontsize=18) +ax1.spines["top"].set_visible(False) +ax1.spines["right"].set_visible(False) +ax2.spines["top"].set_visible(False) +ax2.spines["right"].set_visible(False) fig.tight_layout() -plt.show() -#plt.savefig('stimulus_chirp.png') +#plt.show() +plt.savefig('stimulus_chirp.png') From 4d5110c4b971e17477af85b5af910dab9af18fe0 Mon Sep 17 00:00:00 2001 From: efish Date: Fri, 30 Nov 2018 10:00:00 +0100 Subject: [PATCH 3/4] buh --- code/eod_chirp_beat.py | 4 ++-- code/eod_freq_beat.py | 4 ++-- code/plot_eodform_spikehist.py | 11 +++++------ code/repetition_firingrate.py | 8 ++++---- code/stimulus_chirp.py | 4 ++-- 5 files changed, 15 insertions(+), 16 deletions(-) diff --git a/code/eod_chirp_beat.py b/code/eod_chirp_beat.py index 072cca7..2ff6e6d 100644 --- a/code/eod_chirp_beat.py +++ b/code/eod_chirp_beat.py @@ -81,8 +81,8 @@ ax3.set_ylabel('EOD [mV]', fontsize=22) ax3.xaxis.set_tick_params(labelsize=18) ax3.yaxis.set_tick_params(labelsize=18) -ax3.set_xlabel('time [ms]', fontsize=22) -ax4.set_xlabel('time [ms]', fontsize=22) +ax3.set_xlabel('Time [ms]', fontsize=22) +ax4.set_xlabel('Time [ms]', fontsize=22) ax4.xaxis.set_tick_params(labelsize=18) ax4.set_yticklabels([]) diff --git a/code/eod_freq_beat.py b/code/eod_freq_beat.py index 71e42cc..5e3241d 100644 --- a/code/eod_freq_beat.py +++ b/code/eod_freq_beat.py @@ -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][p]*1000, ampl[p], 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) -ax.set_ylabel("eod amplitude [mV]", fontsize = 22) +ax.set_ylabel("EOD amplitude [mV]", fontsize = 22) plt.yticks(fontsize = 18) ax.spines["top"].set_visible(False) ax.spines["right"].set_visible(False) diff --git a/code/plot_eodform_spikehist.py b/code/plot_eodform_spikehist.py index e7a5cdd..49b0652 100644 --- a/code/plot_eodform_spikehist.py +++ b/code/plot_eodform_spikehist.py @@ -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] @@ -37,9 +36,9 @@ interspikeintervals = np.diff(spikes)/eod_duration 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.xlabel("eod cycles", fontsize = 22) +plt.xlabel("EOD cycles", fontsize = 22) plt.xticks(fontsize = 18) -plt.ylabel("number of \n interspikeintervals", fontsize = 22) +plt.ylabel("Number of \n interspikeintervals", fontsize = 22) plt.yticks(fontsize = 18) ax.spines["top"].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 fig, ax1 = plt.subplots(figsize=(20/inch_factor, 10/inch_factor)) ax1.hist(spike_times, color='firebrick') -ax1.set_xlabel('time [ms]', fontsize=22) -ax1.set_ylabel('number', fontsize=22) +ax1.set_xlabel('Time [ms]', fontsize=22) +ax1.set_ylabel('Number', fontsize=22) ax1.tick_params(axis='y', labelcolor='firebrick') plt.xticks(fontsize=18) plt.yticks(fontsize=18) @@ -101,7 +100,7 @@ ax1.spines['top'].set_visible(False) ax2 = ax1.twinx() 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.set_ylabel('voltage [mV]', fontsize=22) +ax2.set_ylabel('Voltage [mV]', fontsize=22) ax2.tick_params(axis='y', labelcolor='royalblue') ax2.spines['top'].set_visible(False) diff --git a/code/repetition_firingrate.py b/code/repetition_firingrate.py index 30d8b41..9dee716 100644 --- a/code/repetition_firingrate.py +++ b/code/repetition_firingrate.py @@ -8,7 +8,7 @@ from IPython import embed # define sampling rate and data path sampling_rate = 40 #kHz data_dir = "../data" -dataset = "2018-11-09-ad-invivo-1" +dataset = "2018-11-14-al-invivo-1" inch_factor = 2.54 # parameters for binning, smoothing and plotting 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[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].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[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].set_ylabel('firing rate [Hz]', fontsize=22) + ax[1].set_ylabel('Firing rate [Hz]', fontsize=22) plt.xticks(fontsize=18) plt.yticks(fontsize=18) fig.tight_layout() diff --git a/code/stimulus_chirp.py b/code/stimulus_chirp.py index 4558c3d..4ae0f61 100644 --- a/code/stimulus_chirp.py +++ b/code/stimulus_chirp.py @@ -47,8 +47,8 @@ ax1.set_ylabel("field [mV]", fontsize = 22) ax1.yaxis.set_label_coords(-0.1, 0.5) -ax2.set_xlabel("time [ms]", fontsize = 22) -ax2.set_ylabel("frequency [Hz]", fontsize = 22) +ax2.set_xlabel("Time [ms]", fontsize = 22) +ax2.set_ylabel("Frequency [Hz]", fontsize = 22) ax2.yaxis.set_label_coords(-0.1, 0.5) plt.xticks(fontsize=18) plt.yticks(fontsize=18) From 416ef81e85e9f49227c446b025b181623654d69e Mon Sep 17 00:00:00 2001 From: efish Date: Fri, 30 Nov 2018 16:06:32 +0100 Subject: [PATCH 4/4] buh --- code/plot_eodform_spikehist.py | 4 ++-- code/stimulus_chirp.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/code/plot_eodform_spikehist.py b/code/plot_eodform_spikehist.py index 49b0652..3a1a0e6 100644 --- a/code/plot_eodform_spikehist.py +++ b/code/plot_eodform_spikehist.py @@ -9,8 +9,8 @@ from IPython import embed inch_factor = 2.54 sampling_rate = 40000 data_dir = '../data' -#dataset = '2018-11-09-ad-invivo-1' -dataset = '2018-11-14-ad-invivo-1' +dataset = '2018-11-09-ad-invivo-1' +#dataset = '2018-11-14-ad-invivo-1' # read eod and time of baseline time, eod = read_baseline_eod(os.path.join(data_dir, dataset)) diff --git a/code/stimulus_chirp.py b/code/stimulus_chirp.py index 4ae0f61..89d0082 100644 --- a/code/stimulus_chirp.py +++ b/code/stimulus_chirp.py @@ -43,7 +43,7 @@ plt.setp(ax1.get_xticklabels(), visible=False) ax1.plot(time*1000, signal, color = 'royalblue', lw = 1) ax2.plot(time*1000, freq, color = 'royalblue', lw = 3) -ax1.set_ylabel("field [mV]", fontsize = 22) +ax1.set_ylabel("Field [mV]", fontsize = 22) ax1.yaxis.set_label_coords(-0.1, 0.5)