import numpy, array #,rpy2 from matplotlib import pyplot as plt import numpy as np from scipy.optimize import least_squares #from rpy2.robjects.packages import importr #import rpy2.robjects as robjects #import rpy2.robjects.numpy2ri #import notch from numpy.fft import fft, fftfreq # We know/can calculate frequency peak, use this to guess where picks will be. # maybe have a sliding window that reports peak values. def peakPicker(data, omega, dt): # compute window based on omega and dt # make sure you are not aliased, grab every other peak window = (2*numpy.pi) / (omega*dt) data = numpy.array(data) peaks = [] troughs = [] times = [] times2 = [] indices = [] ws = 0 we = window ii = 0 for i in range((int)(len(data)/window)): # initially was just returning this I think avg is better #times.append( (ws + numpy.abs(data[ws:we]).argmax()) * dt ) peaks.append(numpy.max(data[ws:we])) times.append( (ws + data[ws:we].argmax()) * dt ) indices.append( ii + data[ws:we].argmax() ) troughs.append(numpy.min(data[ws:we])) times2.append( (ws + (data[ws:we]).argmin()) * dt ) indices.append( ii + data[ws:we].argmin() ) ws += window we += window ii += (int)(we-ws) #return numpy.array(peaks), numpy.array(times) # Averaging peaks does a good job of removing bias in noise return (numpy.array(peaks)-numpy.array(troughs))/2., \ (numpy.array(times)+numpy.array(times2))/2., \ indices def fun(x, t, y): """ Cost function for regression, single exponential, no DC term x[0] = A0 x[1] = zeta x[2] = df x[3] = T2 """ # concatenated real and imaginary parts return y - np.concatenate((-x[0]*np.sin(2.*np.pi*x[2]*t + x[1])*np.exp(-t/x[3]), \ +x[0]*np.cos(2.*np.pi*x[2]*t + x[1])*np.exp(-t/x[3]))) def fun2(x, t, y): """ Cost function for regression, single exponential, no DC term x[0] = A0 x[1] = zeta x[2] = T2 """ # concatenated real and imaginary parts pre = np.concatenate((x[0]*np.cos(x[1])*np.exp(-t/x[2]), \ -x[0]*np.sin(x[1])*np.exp(-t/x[2]))) return y-pre def quadratureDetect2(X, Y, tt, method, loss, x0="None"): """ Pure python quadrature detection using Scipy. X = real part of NMR signal Y = imaginary component of NMR signal tt = time """ #method = ['trf','dogbox','lm'][method_int] #loss = ['linear','soft_l1','cauchy','huber'][loss_int] #print ("method", method, 'loss', loss) if x0=="None": if method == 'lm': x0 = np.array( [50., 0., 0., .200] ) # A0, zeta, df, T2 res_lsq = least_squares(fun, x0, args=(tt, np.concatenate((X, Y))), loss=loss, f_scale=1.0,\ method=method ) else: x0 = np.array( [50., 0., 0., .200] ) # A0, zeta, df, T2 res_lsq = least_squares(fun, x0, args=(tt, np.concatenate((X, Y))), loss=loss, f_scale=1.0,\ bounds=( [5, -np.pi, -5, .001] , [5000., np.pi, 5, .800] ), method=method ) x = res_lsq.x #print ("A0={} zeta={} df={} T2={}".format(x[0],x[1],x[2],x[3])) else: res_lsq = least_squares(fun, x0, args=(tt, np.concatenate((X, Y))), loss=loss, f_scale=1.0,\ #bounds=( [1., -np.pi, -5, .005] , [1000., np.pi, 5, .800] ), method=method ) #bounds=( [0., 0, -20, .0] , [1., np.pi, 20, .6] )) x = res_lsq.x return res_lsq.success, x[0], x[2], x[1], x[3] # no df #x = np.array( [1., 0., 0.2] ) #res_lsq = least_squares(fun2, x, args=(tt, np.concatenate((X, Y))), loss='soft_l1', f_scale=0.1) #x = res_lsq.x #return conv, E0,df,phi,T2 #return res_lsq.success, x[0], 0, x[1], x[2] ################################################################### ################################################################### ################################################################### if __name__ == "__main__": dt = .0001 T2 = .1 omega = 2000.*2*numpy.pi phi = .0 T = 8.*T2 t = numpy.arange(0, T, dt) # Synthetic data, simple single decaying sinusoid # with a single decay parameter and gaussian noise added data = numpy.exp(-t/T2) * numpy.sin(omega * t + phi) + numpy.random.normal(0,.05,len(t)) \ + numpy.random.randint(-1,2,len(t))*numpy.random.exponential(.2,len(t)) cdata = numpy.exp(-t/T2) * numpy.sin(omega * t + phi) #+ numpy.random.normal(0,.25,len(t)) #data = numpy.random.normal(0,.25,len(t)) sigma2 = numpy.std(data[::-len(data)/4]) #sigma2 = numpy.var(data[::-len(data)/4]) print("sigma2", sigma2) [peaks,times,indices] = peakPicker(data, omega, dt) [b1,b2,rT2] = regressCurve(peaks,times) print("rT2 nonweighted", rT2) [b1,b2,rT2] = regressCurve(peaks,times,sigma2) print("rT2 weighted", rT2) envelope = numpy.exp(-t/T2) renvelope = numpy.exp(-t/rT2) #outf = file('regress.txt','w') #for i in range(len(times)): # outf.write(str(times[i]) + " " + str(peaks[i]) + "\n") #outf.close() plt.plot(t,data, 'b') plt.plot(t,cdata, 'g', linewidth=1) plt.plot(t,envelope, color='violet', linewidth=4) plt.plot(t,renvelope, 'r', linewidth=4) plt.plot(times, numpy.array(peaks), 'bo', markersize=8, alpha=.25) plt.legend(['noisy data','clean data','real envelope','regressed env','picks']) plt.savefig("regression.pdf") # FFT check fourier = fft(data) plt.figure() freq = fftfreq(len(data), d=dt) plt.plot(freq, (fourier.real)) plt.show() # TODO do a bunch in batch mode to see if T2 estimate is better with or without # weighting and which model is best. # TODO try with real data # TODO test filters (median, FFT, notch) # It looks like weighting is good for relatively low sigma, but for noisy data # it hurts us. Check