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Nanopore-tools/MakeIndividualIVs.py
b69207051934Development-of-Analysis…

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MakeIndividualIVs.py
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import numpy as np
import scipy
import scipy.signal as sig
import Functions as uf
import pyqtgraph as pg
import os
import matplotlib.pyplot as plt
import matplotlib
from tkinter import Tk
from tkinter.filedialog import askopenfilenames
from matplotlib.font_manager import FontProperties
fontP = FontProperties()
fontP.set_size('small')
props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
from matplotlib.ticker import EngFormatter
Res = EngFormatter(unit=r'$\frac{kg\cdot m^2}{A\cdot C\cdot s^2}$', places=2)
Cond = EngFormatter(unit=r'$\frac{A\cdot C\cdot s^2}{kg\cdot m^2}$', places=2)
size = EngFormatter(unit='m', places=2)
Tk().withdraw()
os.system('''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' ''')
expname = 'All'
reversePolarity = 0
PoreSize = [10, 1e-9]
filenames = askopenfilenames() # show an "Open" dialog box and return the path to the selected file
for filename in filenames:
print(filename)
#Make Dir to save images
output = uf.OpenFile(filename)
if reversePolarity:
print('Polarity Reversed!!!!')
output['i1']= -output['i1']
output['v1']= -output['v1']
directory = (str(os.path.split(filename)[0]) + os.sep + expname + '_SavedImages')
if not os.path.exists(directory):
os.makedirs(directory)
AllData = uf.MakeIVData(output, delay = 3)#, UseVoltageRange = [-0.4, 0.4])
if AllData == 0:
print('!!!! No Sweep in: ' + filename)
continue
#Plot Considered Part
#figExtracteParts = plt.figure(1)
#ax1 = figExtracteParts.add_subplot(211)
#ax2 = figExtracteParts.add_subplot(212, sharex=ax1)
#(ax1, ax2) = uf.PlotExtractedPart(output, AllData, current = 'i1', unit=1e9, axis = ax1, axis2=ax2)
#plt.show()
#figExtracteParts.savefig(directory + os.sep + 'PlotExtracted_' + str(os.path.split(filename)[1])[:-4] + '.eps')
#figExtracteParts.savefig(directory + os.sep + 'PlotExtracted_' + str(os.path.split(filename)[1])[:-4] + '.png', dpi=150)
# Plot IV
if output['graphene']:
figIV2 = plt.figure(3, figsize=(10, 10))
figIV2.clear()
ax2IV = figIV2.add_subplot(111)
ax2IV = uf.PlotIV(output, AllData, current='i2', unit=1e9, axis=ax2IV, WithFit=1)
figIV2.tight_layout()
figIV2.savefig(directory + os.sep + str(os.path.split(filename)[1]) + '_IV_i2.png', dpi=300)
figIV2.savefig(directory + os.sep + str(os.path.split(filename)[1]) + '_IV_i2.eps')
figIV = plt.figure(2, figsize=(10, 7))
ax1IV = figIV.add_subplot(111)
current = 'i1'
#ax1IV = uf.PlotIV(output, AllData, current='i1', unit=1, axis = ax1IV, WithFit = 1, useEXP = 0, color ='y',
# labeltxt='MeanFit', PoreSize=[10, 1e-9], title=str(os.path.split(filename)[1]))
textstr = 'Pore Size\nConductance: {}S/m\nLenght: {}m:\ndiameter: {}m'.format(size.format_data(PoreSize[0]),
pg.siFormat(PoreSize[1]), pg.siFormat(uf.CalculatePoreSize(AllData[current]['YorkFitValues']['Slope'], PoreSize[1], PoreSize[0])))
ax1IV.text(0.05, 0.95, textstr, transform=ax1IV.transAxes, fontsize=12,
verticalalignment='top', bbox=dict(boxstyle='round', facecolor='wheat', alpha=0.5))
ind = np.argsort(AllData[current]['Voltage'])
p = np.polyfit(AllData[current]['Voltage'][ind], AllData[current]['Mean'][ind], 1)
ax1IV.errorbar(AllData[current]['Voltage'][ind], AllData[current]['Mean'][ind],
yerr=AllData[current]['STD'][ind], fmt='o', color='b')
ax1IV.plot(AllData[current]['Voltage'][ind], np.polyval(p, AllData[current]['Voltage'][ind]), color='r')
ax1IV.set_title(str(os.path.split(filename)[1])+ '\nR=' + Res.format_data(1/p[0]) + ', G=' + Cond.format_data(p[0]))
ax1IV.set_ylabel('Current')
ax1IV.set_xlabel('Voltage')
ax1IV.xaxis.set_major_formatter(EngFormatter(unit=r'$\frac{kg\cdot m^2}{A\cdot s^3}$'))
ax1IV.yaxis.set_major_formatter(EngFormatter(unit=r'$\frac{C}{s}$'))
figIV.savefig(directory + os.sep + str(os.path.split(filename)[1]) + 'IV_i1.pdf', transparent=True)
plt.show()
figIV.clear()
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