17.08

jar_functions.py

@@ -102,8 +102,8 @@ def mean_noise_cut(frequencies, time, n):
     cutf = []
     cutt = []
     for k in np.arange(0, len(frequencies), n):
-        t = time[k]
         f = np.mean(frequencies[k:k+n])
+        t = time[k]
         cutf.append(f)
         cutt.append(t)
     return cutf, cutt

sin_response_fit.py

@@ -6,11 +6,14 @@ from IPython import embed
 from scipy.optimize import curve_fit
 from jar_functions import sin_response
 
-def take_second(elem):
+def take_second(elem):      # function for taking the names out of files
     return elem[1]
 
 predict = []
 
+rootmeansquare = []
+threshold = []
+
 gain = []
 mgain = []
 phaseshift = []
@@ -21,35 +24,38 @@ amf = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1]
 currf = None
 idxlist = []
 
-data = sorted(np.load('files.npy'), key = take_second)
+data = sorted(np.load('files.npy'), key = take_second)      # list with filenames in it
 
 for i, d in enumerate(data):
     dd = list(d)
-    jar = np.load('%s.npy' %dd)
-    jm = jar - np.mean(jar)
+    jar = np.load('%s.npy' %dd)     # load data for every file name
+    jm = jar - np.mean(jar)         # low-pass filtering by subtracting mean
     print(dd)
 
-    time = np.load('time: %s.npy' %dd)
+    time = np.load('%s time.npy' %dd)       # time file
 
-    b, a = signal.butter(4, (float(d[1]) / 2) / 10000, 'high', analog=True)
+    b, a = signal.butter(4, (float(d[1]) / 2) / 10000, 'high', analog=True)     # high pass filtering so our fit gets a bit better
     y = signal.filtfilt(b, a, jm)
     #plt.plot(time, y)
     #plt.plot(time, jar)
 
-    sinv, sinc = curve_fit(sin_response, time, y, [float(d[1]), 2, 0.5])
+    sinv, sinc = curve_fit(sin_response, time, y, [float(d[1]), 2, 0.5])        # fitting
     print('frequency, phaseshift, amplitude:', sinv)
+    plt.show()
+    p = np.sqrt(sinv[1]**2)
+    A = np.sqrt(sinv[2] ** 2)
+    f = float(d[1])
+    phaseshift.append(p)
+    gain.append(A)
+    amfreq.append(f)
 
-    phaseshift.append(np.sqrt(sinv[1]**2))
-    gain.append(np.sqrt(sinv[2]**2))
-    amfreq.append(d[1])
+    # root mean square
 
-    Rs = []
-    for ix, t in enumerate(time):
-        R = (jm[ix] - sin_response(t, float(d[1]), np.sqrt(sinv[1]**2), np.sqrt(sinv[2]**2)))**2
-        Rs.append(R)
+    RMS = np.sqrt(np.mean((jm - sin_response(time, sinv[0], sinv[1], sinv[2]))**2))
+    rootmeansquare.append(RMS)
+    thresh = A / np.sqrt(2)
+    threshold.append(thresh)
 
-    sigma = sum(Rs)
-    rms = np.sqrt((1/len(time)) * sigma)
     #plt.plot(time, sin_response(time, *sinv), label='fit: f=%f, p=%.2f, A=%.2f' % tuple(sinv))
 
     #mean over same amfreqs for phase and gain
@@ -80,6 +86,7 @@ meanedp = np.mean(meanp)
 mgain.append(meanedf)
 mphaseshift.append(meanedp)
 
+# predict of gain
 for f in amf:
     G = np.max(mgain) / np.sqrt(1 + (2*((np.pi*f*3.14)**2)))
     predict.append(G)
@@ -89,16 +96,24 @@ for f in amf:
 fig = plt.figure()
 ax = fig.add_subplot(1, 1, 1)
 ax.plot(amf, mgain, 'o')
-ax.plot(amf, predict)
+#ax.plot(amf, predict)
 ax.set_yscale('log')
 ax.set_xscale('log')
-ax.set_title('2018lepto98')
+ax.set_title('%s' % data[0][0])
 ax.set_ylabel('gain [Hz/(mV/cm)]')
 ax.set_xlabel('AM-frequency [Hz]')
-#plt.savefig('2018lepto98_gain')
+#plt.savefig('%s gain' % data[0][0])
 pylab.show()
+plt.plot(threshold, label = 'threshold')
+plt.plot(rootmeansquare, label = 'RMS')
+plt.legend()
+plt.show()
 embed()
 
 #phase in degree
 # Q10 / conductivity
 # AM-frequency / envelope-frequency scale title?
+
+# bevor fit noch filtern mit 15Hz damit AM-Modulation rausgefiltert wird und nur noch envelope übrig bleibt.
+# Dazu running average mit n wobei n über samplingrate und delta f bestimmt wird
+# samplingrate über overlap muss dabei aber größer sein als samplingrate die noch übrig bleibt wenn ich mit delta f frequency gefiltert hab

sin_response_specto.py

@@ -21,23 +21,22 @@ from jar_functions import average
 from jar_functions import import_data
 from jar_functions import import_amfreq
 
-base_path = 'D:\\jar_project\\JAR\\sin\\2018lepto98'
+base_path = 'D:\\jar_project\\JAR\\sin\\2020lepto16'
 
 #nicht: -5Hz delta f, 19-aa, 22-ae, 22-ad (?)
 
 #dat = glob.glob('D:\\jar_project\\JAR\\2020*\\beats-eod.dat')
 #infodat = glob.glob('D:\\jar_project\\JAR\\2020*\\info.dat')
-datasets = ['2020-07-21-ak',
-'2020-07-21-al',
-'2020-07-21-am',
-'2020-07-21-an',
-'2020-07-21-ao',
-'2020-07-22-ai',
-'2020-07-22-aj',
-'2020-07-22-ak',
-'2020-07-22-al',
-'2020-07-22-am',
-            ]
+datasets = ['2020-08-04-ab',
+            '2020-08-04-ac',
+            '2020-08-04-ad',
+            '2020-08-04-ae',
+            '2020-08-04-af',
+            '2020-08-05-ab',
+            '2020-08-05-ac',
+            '2020-08-05-ad',
+            '2020-08-05-ae',
+            '2020-08-05-af']
 
 time_all = []
 freq_all = []
@@ -106,11 +105,16 @@ for idx, dataset in enumerate(datasets):
         freq4 = freqs[ix0:ix1]
         jar4 = freq4[np.argmax(spec4, axis=0)]      # all freqs at max specs over axis 0
         jar = jar4 / 4
-        jm = jar4 - np.mean(jar4)
+        jm = jar4 - np.mean(jar4)   # data we take
 
         cut_times = times[:len(jar4)]
-        np.save('time: %s.npy' % file_name, cut_times)
-        np.save('%s.npy' % file_name, jar4)
+        np.save('%s time' % file_name, cut_times)
+        np.save('%s' % file_name, jar4)
+
+        cutf, cutt = mean_noise_cut(jar4, cut_times, 40000 * (1/15))
+        plt.plot(cutt, cutf)
+        plt.show()
+        embed()
 
         #plt.plot(cut_times, jm, '-k')