diff --git a/code/eod_freq_normal.py b/code/eod_freq_normal.py index 7b0e192..5228031 100644 --- a/code/eod_freq_normal.py +++ b/code/eod_freq_normal.py @@ -5,7 +5,13 @@ import numpy as np data_dir = '../data' #dataset = '2018-11-09-ad-invivo-1' -data = ["2018-11-09-ad-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1"] +data = ["2018-11-09-ad-invivo-1", + "2018-11-13-aa-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", + "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", + "2018-11-14-ac-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ak-invivo-1", + "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", + "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-af-invivo-1", + "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1"] for dataset in data: # read eod and time of baseline diff --git a/code/plot_eodform_spikehist.py b/code/plot_eodform_spikehist.py index 44892bc..24d3590 100644 --- a/code/plot_eodform_spikehist.py +++ b/code/plot_eodform_spikehist.py @@ -8,7 +8,8 @@ from IPython import embed # plot and data values inch_factor = 2.54 data_dir = '../data' -dataset = '2018-11-09-ad-invivo-1' +#dataset = '2018-11-09-ad-invivo-1' +dataset = '2018-11-14-al-invivo-1' # read eod and time of baseline time, eod = read_baseline_eod(os.path.join(data_dir, dataset)) @@ -29,8 +30,9 @@ plt.yticks(fontsize = 18) ax.spines["top"].set_visible(False) ax.spines["right"].set_visible(False) fig.tight_layout() +plt.show() #plt.show() -plt.savefig('isis.pdf') +#plt.savefig('isis.pdf') exit() # calculate coefficient of variation diff --git a/code/response_beat.py b/code/response_beat.py index e57b1c7..a8837e3 100644 --- a/code/response_beat.py +++ b/code/response_beat.py @@ -1,6 +1,7 @@ import matplotlib.pyplot as plt import numpy as np from read_chirp_data import * +from read_baseline_data import * from utility import * from IPython import embed @@ -11,27 +12,37 @@ cut_window = 40 cut_range = np.arange(-cut_window * sampling_rate, 0, 1) window = 1 -''' -# norm: -150, 150, 300 -data = ["2018-11-13-aa-invivo-1", "2018-11-13-ac-invivo-1","2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", - "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1"] +# norm: -150, 150, 300 aa, #ac, aj?? +data = ["2018-11-13-al-invivo-1"]#, "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", + #"2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1"] +''' # norm: -50 data = ["2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1","2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1"] -''' data = ["2018-11-14-aa-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ah-invivo-1", "2018-11-14-ai-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1"] +''' +#data = ["2018-11-09-ad-invivo-1", "2018-11-14-af-invivo-1"] rates = {} for dataset in data: + print(dataset) + # read baseline spikes + base_spikes = read_baseline_spikes(os.path.join(data_dir, dataset)) + base_spikes = base_spikes[1000:2000] + spikerate = len(base_spikes)/base_spikes[-1] + print(spikerate) + + # read spikes during chirp stimulation spikes = read_chirp_spikes(os.path.join(data_dir, dataset)) df_map = map_keys(spikes) - print(dataset) + + # iterate over df for df in df_map.keys(): ''' if df == 50: @@ -39,8 +50,8 @@ for dataset in data: else: continue ''' - - print(df) + + #print(df) rep_rates = [] beat_duration = int(abs(1 / df) * 1000) beat_window = 0 @@ -56,9 +67,12 @@ for dataset in data: binary_spikes = np.isin(cut_range, spikes_idx) * 1 smoothed_data = smooth(binary_spikes, window, 1 / sampling_rate) train = smoothed_data[window:beat_window+window] - rep_rates.append(np.std(train)) + norm_train = train*1000#/spikerate + rep_rates.append(np.std(norm_train))#/spikerate) break - df_rate = np.mean(rep_rates) + df_rate = np.median(rep_rates)/spikerate + #embed() + #exit() if df in rates.keys(): rates[df].append(df_rate) else: