diff --git a/jar_functions.py b/jar_functions.py index 0c73330..4edb410 100644 --- a/jar_functions.py +++ b/jar_functions.py @@ -2,6 +2,15 @@ import os #compability with windows from IPython import embed import numpy as np +def step_response(t, a1, a2, tau1, tau2): + r_step = (a1*(1 - np.exp(-t/tau1))) + (a2*(1 - np.exp(-t/tau2))) + r_step[t<0] = 0 + return r_step + +def sin_response(t, f, p, A): + r_sin = A*sin(2*np.pi*t*f + p) + return r_sin + def parse_dataset(dataset_name): assert(os.path.exists(dataset_name)) #see if data exists f = open(dataset_name, 'r') #open data we gave in @@ -100,12 +109,6 @@ def mean_noise_cut(frequencies, time, n): cutt.append(t) return cutf, cutt - -def step_response(t, a1, a2, tau1, tau2): - r_step = (a1*(1 - np.exp(-t/tau1))) + (a2*(1 - np.exp(-t/tau2))) - r_step[t<0] = 0 - return r_step - def norm_function(cf_arr, ct_arr, onset_point, offset_point): onset_end = onset_point - 10 offset_start = offset_point - 10 diff --git a/second_try.py b/second_try.py deleted file mode 100644 index 9d0de30..0000000 --- a/second_try.py +++ /dev/null @@ -1,112 +0,0 @@ -import matplotlib.pyplot as plt -import os -import glob -import IPython -import numpy as np -from IPython import embed -from scipy.optimize import curve_fit -from jar_functions import parse_dataset -from jar_functions import parse_infodataset -from jar_functions import mean_traces -from jar_functions import mean_noise_cut -from jar_functions import norm_function -from jar_functions import step_response -from jar_functions import sort_values - -#nicht: 19-aa, 22-ae, 22-ad (?) -datasets = [#(os.path.join('D:\\jar_project\\JAR\\2020-06-19-aa\\beats-eod.dat')), #-5Hz delta f, horrible fit - #(os.path.join('D:\\jar_project\\JAR\\2020-06-19-ab\\beats-eod.dat')), #-5Hz delta f, bad fit - #(os.path.join('D:\\jar_project\\JAR\\2020-06-22-aa\\beats-eod.dat')), #-5Hz delta f, bad fit - #(os.path.join('D:\\jar_project\\JAR\\2020-06-22-ab\\beats-eod.dat')), #-5Hz delta f, bad fit - (os.path.join('D:\\jar_project\\JAR\\2020-06-22-ac\\beats-eod.dat')), #-15Hz delta f, good fit - #(os.path.join('D:\\jar_project\\JAR\\2020-06-22-ad\\beats-eod.dat')), #-15Hz delta f, horrible fit - #(os.path.join('D:\\jar_project\\JAR\\2020-06-22-ae\\beats-eod.dat')), #-15Hz delta f, maxfev way to high so horrible - (os.path.join('D:\\jar_project\\JAR\\2020-06-22-af\\beats-eod.dat'))] #-15Hz delta f, good fit - -#np.array(sorted(glob.glob('D:\\jar_project\\JAR\\2020*\\beats-eod.dat'))) - -infodatasets = [(os.path.join('D:\\jar_project\\JAR\\2020-06-22-ac\\info.dat')), - (os.path.join('D:\\jar_project\\JAR\\2020-06-22-af\\info.dat'))] - - -time_all = [] -freq_all = [] - -ID = [] - -for infodataset in infodatasets: - i = parse_infodataset(infodataset) - identifier = i[0] - ID.append(identifier) - - -for idx, dataset in enumerate(datasets): - #input of the function - frequency, time, amplitude, eodf, deltaf, stimulusf, duration, pause = parse_dataset(dataset) - dm = np.mean(duration) - pm = np.mean(pause) - timespan = dm + pm - start = (time[0][0] + time[1][0]) / 2 - stop = (time[0][-1] + time[1][-1]) / 2 - mf , tnew = mean_traces(start, stop, timespan, frequency, time) # maybe fixed timespan/sampling rate - - #for i in range(len(mf)): - - cf, ct = mean_noise_cut(mf, tnew, n=1250) - - cf_arr = np.array(cf) - ct_arr = np.array(ct) - - norm = norm_function(cf_arr, ct_arr, onset_point = dm - dm, offset_point = dm) #dm-dm funktioniert nur wenn onset = 0 sec - - freq_all.append(norm.tolist()) - time_all.append(ct_arr) - - plt.plot(ct_arr, norm, color = 'grey', label='fish=%s' % ID[idx]) - - # fit function - sv, sc = curve_fit(step_response, ct_arr[ct_arr < dm], norm[ct_arr < dm]) #step_values and step_cov - - # sorted a and tau - values = sort_values(sv) - - ''' - plt.plot(ct_arr[ct_arr < 100], step_response(ct_arr, *sv)[ct_arr < 100], color='orange', - label='fit: a1=%.2f, a2=%.2f, tau1=%.2f, tau2=%.2f' % tuple(values)) - ''' - - print('fish: a1, a2, tau1, tau2', values) - -# average over all fish -mf_all , tnew_all = mean_traces(start, stop, timespan, freq_all, time_all) - -plt.plot(tnew_all, mf_all, color = 'b', label = 'average', ls = 'dashed') - -# fit for average -sv_all, sc_all = curve_fit(step_response, tnew_all[tnew_all < dm], mf_all[tnew_all < dm]) #step_values and step_cov - -values_all = sort_values(sv_all) - -plt.plot(tnew_all[tnew_all < 100], step_response(tnew_all, *sv_all)[tnew_all < 100], color='orange', - label='average_fit: a1=%.2f, a2=%.2f, tau1=%.2f, tau2=%.2f' % tuple(values_all)) - -print('average: a1, a2, tau1, tau2', values_all) - -const_line = plt.axhline(y = 0.632) -stimulus_duration = plt.hlines(y = -0.25, xmin = 0, xmax = 100, color = 'r', label = 'stimulus_duration') -base_line = plt.axhline(y = 0, color = 'black', ls = 'dotted', linewidth = '1') - -plt.xlim([-10,220]) -plt.xlabel('time [s]') -plt.ylabel('rel. JAR magnitude') -plt.title('relative JAR') -plt.savefig('relative JAR') -plt.legend(loc = 'lower right') -plt.show() -embed() - -# Fragen: -# wie offset point wenn nicht start bei 0 sec? über zeitdatenpunkt? oder einfach immer bei 0 onset..? -# wie zip ich ID liste mit plot (für eine for schleife) zusammen? -# welche Stimulusintesität? -# start/stop/timespan ok? \ No newline at end of file