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Nanopore-tools/LockInPlotting.py
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LockInPlotting.py
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import matplotlib.pyplot as plt
import numpy as np
import os
import matplotlib
from matplotlib.font_manager import FontProperties
from tkinter import Tk
from matplotlib.ticker import EngFormatter
matplotlib.rcParams['agg.path.chunksize'] = 100000
fontP = FontProperties()
fontP.set_size('small')
props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
Tk().withdraw()
os.system('''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' ''')
filebyfile = 1
expname = 'All'
#filenames = askopenfilenames() # show an "Open" dialog box and return the path to the selected file
filenames={'/Volumes/lben/lben-commun/2018 User Data/Michael/LockIn/modelcell_05-02-2018_14_40.txt', '/Volumes/lben/lben-commun/2018 User Data/Michael/LockIn/2modelcells, resistor_05-02-2018_14_55.txt'}
range = [10, 10e3]
voltage = 100e-3
for file in filenames:
filehandle = open(file, 'r')
(f, V, theta, I, R, C) = np.loadtxt(filehandle, unpack=True)
V = V*1e-3
I = I*1e-9
C = C*1e-9
theta = -theta
print(I)
if range[1]:
ind = np.argwhere((f >= range[0]) & (f <= range[1])).flatten()
print(ind)
f = f[ind]
V = V[ind]
theta = theta[ind]
I = I[ind]
R = R[ind]
C = C[ind]
print(I)
filehandle.close()
figIV = plt.figure(1)
ImpR = voltage/I*np.cos(np.deg2rad(theta))
ImpIm = voltage/I*np.sin(np.deg2rad(theta))
axR = figIV.add_subplot(222)
axR.set_title('Resistance')
axR.set_xlabel('Frequency')
axR.set_ylabel('Resistance')
axR.set_xscale('log')
axR.set_yscale('log')
axR.yaxis.set_major_formatter(EngFormatter(unit='$\Omega$', places=0))
axR.xaxis.set_major_formatter(EngFormatter(unit='Hz', places=0))
axR.plot(f, R)
axC = figIV.add_subplot(224)
axC.set_title('Capacitance')
axC.set_xlabel('Frequency')
axC.set_ylabel('Capacitance')
axC.set_xscale('log')
axC.set_yscale('linear')
axC.yaxis.set_major_formatter(EngFormatter(unit='C', places=0))
axC.xaxis.set_major_formatter(EngFormatter(unit='Hz', places=0))
axC.plot(f, C)
axI = figIV.add_subplot(221)
axI.set_title('Current')
axI.set_xlabel('Frequency')
axI.set_ylabel('Current')
axI.set_xscale('log')
axI.set_yscale('log')
axI.yaxis.set_major_formatter(EngFormatter(unit='A', places=0))
axI.xaxis.set_major_formatter(EngFormatter(unit='Hz', places=0))
axI.plot(f, I)
axT = figIV.add_subplot(223)
axT.set_title('Phase')
axT.set_xlabel('Frequency')
axT.set_ylabel('Phase')
axT.set_xscale('log')
axT.set_yscale('linear')
axT.yaxis.set_major_formatter(EngFormatter(unit='°', places=0))
axT.xaxis.set_major_formatter(EngFormatter(unit='Hz', places=0))
axT.plot(f, theta)
figImp = plt.figure(2)
axNyq = figImp.add_subplot(111)
axNyq.set_title('Nyquist Plot')
axNyq.set_xlabel('Real Part [Re(Z)]')
axNyq.set_ylabel('Imaginary Part [Im(Z)]')
axNyq.plot(ImpR, ImpIm, ls = 'None', marker = 'o')
figIV.savefig(file[:-4] + '10kHz.png', dpi=300)
figImp.savefig(file[:-4] + '_Nyquist10kHz.png', dpi=300)
# plt.show()
figIV.clear()
figImp.clear()
## Save Img, Real and Freq to txt file
np.savetxt(file[:-4] + '_Data10kHz.txt', np.transpose((ImpR, ImpIm, f)), fmt='%.14E', delimiter=' ', newline='\n', header=str(len(ImpIm)), comments='')
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