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Nanopore-tools/MakeIndividualIVs.py
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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
import platform
import csv
import argparse
from pprint import pprint
#Set font properties
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
#Set units formatting
from matplotlib.ticker import EngFormatter
Res = EngFormatter(unit='Ω', places=2)
Cond = EngFormatter(unit='S', places=2)
SpesCond = EngFormatter(unit='S/m', places=2)
size = EngFormatter(unit='m', places=2)
Tk().withdraw()
if (platform.system()=='Darwin'):
os.system('''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' ''')
#Define default parameters for size fitting
expname = 'All'
Parameters = {
'Type': 'Nanopore', #Nanopore, Nanocapillary, NanocapillaryShrunken
'reversePolarity': 0,
'specificConductance': 10.5, #10.5 S/m for 1M KCl
'delay':2, #seconds for reading current
#Nanopore
'poreLength' : 1e-9,
#Nanocapillary
'taperLength' : 3.3e-3,
'innerDiameter' : 0.2e-3,
'taperLengthShaft' : 543e-9,
'innerDiameterShaft' : 514e-9,
#Fit option
'CurveFit' : 'PolyFit' #PolyFit YorkFit
}
def run(filenames,newParameters={}):
for key in newParameters:
Parameters[key]=newParameters[key]
Type=Parameters['Type']
CurveFit=Parameters['CurveFit']
specificConductance=Parameters['specificConductance']
for filename in filenames:
os.chdir(os.path.dirname(filename))
print(filename)
#Make Dir to save images
output = uf.OpenFile(filename)
if Parameters['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, approach='mean', delay = Parameters['delay'])#, 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]))
Slope=AllData[current][CurveFit]['Slope']
Yintercept=AllData[current][CurveFit]['Yintercept']
if Type=='Nanopore':
poreLength=Parameters['poreLength']
textstr = 'Nanopore Size\n\nSpecific Conductance: {}\nLenght: {}\n\nConductance: {}\nDiameter: {}'\
.format(SpesCond.format_data(specificConductance),size.format_data(poreLength), Cond.format_data(Slope),
size.format_data(uf.CalculatePoreSize(Slope, poreLength, specificConductance)))
elif Type=='Nanocapillary':
taperLength=Parameters['taperLength']
innerDiameter=Parameters['innerDiameter']
textstr = 'Nanocapillary Size\n\nSpecific Conductance: {}\nTaper lenght: {}:\nInner diameter: {}:\n\nConductance: {}\nDiameter: {}'.\
format(SpesCond.format_data(specificConductance),size.format_data(taperLength),size.format_data(innerDiameter),Cond.format_data(Slope),
size.format_data(uf.CalculateCapillarySize(Slope, innerDiameter, taperLength, specificConductance)))
elif Type=='NanocapillaryShrunken':
taperLength=Parameters['taperLength']
innerDiameter=Parameters['innerDiameter']
taperLengthShaft=Parameters['taperLengthShaft']
innerDiameterShaft=Parameters['innerDiameterShaft']
NCSize=uf.CalculateShrunkenCapillarySize(Slope,innerDiameter, taperLength,specificConductance,taperLengthShaft,innerDiameterShaft)
textstr = 'Shrunken Nanocapillary Size\n\nSpecific Conductance: {}\nTaper lenght: {}\nInner diameter: {}\nTaper length at shaft: {}' \
'\nInner Diameter at shaft: {}:\n\nConductance: {}\nDiameter: {}'.\
format(SpesCond.format_data(specificConductance),size.format_data(taperLength),size.format_data(innerDiameter),
size.format_data(taperLengthShaft),size.format_data(innerDiameterShaft), Cond.format_data(Slope),
size.format_data(NCSize))
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'])
ax1IV.errorbar(AllData[current]['Voltage'][ind], AllData[current]['Mean'][ind],
yerr=AllData[current]['SE'][ind], fmt='o', color='b')
ax1IV.plot(AllData[current]['Voltage'][ind], np.polyval([Slope,Yintercept], AllData[current]['Voltage'][ind]), color='r')
ax1IV.set_title(str(os.path.split(filename)[1])+ '\nR=' + Res.format_data(1/Slope) + ', G=' + Cond.format_data(Slope))
ax1IV.set_ylabel('Current')
ax1IV.set_xlabel('Voltage')
ax1IV.xaxis.set_major_formatter(EngFormatter(unit='V'))
ax1IV.yaxis.set_major_formatter(EngFormatter(unit='A'))
figIV.savefig(directory + os.sep + str(os.path.split(filename)[1]) + Type+'IV_i1.pdf', transparent=True)
x=AllData[current]['Voltage'][ind]
y=AllData[current]['Mean'][ind]
csvfile=directory + os.sep + str(os.path.split(filename)[1]) + Type+'IV_i1.csv'
with open(csvfile, 'w') as output:
writer=csv.writer(output, lineterminator='\n')
for i in range(len(x)):
writer.writerow([x[i] , y[i]])
plt.show()
figIV.clear()
if __name__=='__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', help='input file')
parser.add_argument('-c', '--coeff',
help='Coefficients for calculating pore size',
nargs='+')
parser
args = parser.parse_args()
inputData=args.input
if inputData==None:
inputData=askopenfilenames()
else:
inputData={inputData}
newParameters={}
if args.coeff is not None:
if len(args.coeff) % 2 == 0:
for i in range(0, len(args.coeff), 2):
if i <= len(args.coeff):
newParameters[str(args.coeff[i])]=args.coeff[i+1]
run(inputData,newParameters)
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