bruteforce

Author: markgarnold

nintan/markbruteforce.py

@@ -0,0 +1,49 @@
+import utils_concore 
+import numpy as np
+import matplotlib.pyplot as plt
+import concore
+
+FREQ_BINS = 25
+
+def brute_freqs(filename):
+    y, yextra2, yextra3 = utils_concore.read_trellis_data([filename+'.nf3'],channums=[1,2,3,4])  
+    plt.figure()
+    plt.subplot(411)
+    plt.plot(range(len(y[0])),y[0])
+    #plt.xlabel('Gastric 1')
+    plt.subplot(412)
+    plt.plot(range(len(y[1])),y[1])
+    #plt.xlabel('Gastric 2')
+    plt.subplot(413)
+    plt.plot(range(len(y[2])),y[2])
+    #plt.xlabel('Gastric 3')
+    plt.subplot(414)
+    plt.plot(range(len(y[3])),y[3])
+    plt.xlabel('Raw file:'+filename+ ' iteration '+str(concore.simtime))
+    plt.savefig(filename+str(concore.simtime)+"r.pdf")
+
+    result = []
+    plt.figure()
+    plt.subplot(411)
+    result.append(smooth_freq(y,0,FREQ_BINS))
+    plt.subplot(412)
+    result.append(smooth_freq(y,1,FREQ_BINS))
+    plt.subplot(413)
+    result.append(smooth_freq(y,2,FREQ_BINS))
+    plt.subplot(414)
+    result.append(smooth_freq(y,3,FREQ_BINS))
+    plt.xlabel('Freq:'+filename+ ' iteration '+str(concore.simtime))
+    plt.savefig(filename+str(concore.simtime)+"f.pdf")
+    #plt.show()
+    return result
+
+def smooth_freq(y,chan,bins):
+    f=np.fft.fft(y[chan])
+    f0=np.abs(f[-(bins-1):-1])
+    f1=np.abs(f[-bins:-2])
+    f2=np.abs(f[-(bins+1):-3])
+    fa=f2+2*f1+f2
+#    plt.plot(np.arange(bins,2,-1),np.log(np.abs(fa)))
+    return bins-np.argmax((np.abs(fa)))
+
+

nintan/smoothfreq.py

@@ -0,0 +1,15 @@
+import numpy as np
+
+def smooth_freq(y,bins):
+    f=np.fft.fft(y)
+    f0=np.abs(f[-(bins-1):-1])
+    f1=np.abs(f[-bins:-2])
+    f2=np.abs(f[-(bins+1):-3])
+    fa=f2+2*f1+f2
+    return bins-np.argmax((np.abs(fa)))
+
+def dom_freq(y,t):
+    ttot = (t[-1] - t[0]) * len(y)/(len(y)-1)
+    f = np.fft.fft(y)
+    fi = np.argmax((np.abs(f)))
+    return np.fft.fftfreq(len(y))[fi]*len(y)/ttot