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MakeIndividualIVs.py
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Sat, Apr 20, 08:45

MakeIndividualIVs.py
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# -*- coding: utf-8 -*-
import numpy as np
import Functions as uf
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
import LoadData
#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)
if (platform.system()=='Darwin'):
Tk().withdraw()
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': 3, # seconds for reading current
# Nanopore
'poreLength': 20e-9,
# Nanocapillary
'taperLength': 3.3e-3,
'innerDiameter': 0.2e-3,
'taperLengthShaft': 543e-9,
'innerDiameterShaft': 514e-9,
# Fit option
'CurveFit': 'PolyFit', # PolyFit YorkFit
'fittingMethod': 'mean' # expFit, mean
}
def GetParameters():
print("Usage:")
print("run(filenames,newParameters={},verbose=False, noPlot=False")
print('Returns poresize in m')
print()
print("Default Parameters:")
pprint(Parameters)
def run(filenames, newParameters={}, verbose=False, noPlot=False):
"""
Function used to call all the necessary other functions to make I-V curves.
It takes a list of filenames as necessary argument. For each data file, a corresponding
I-V curve will be generated.
It iterates on the filenames in the list and calls the corresponding MakeIVData from
Functions module.
Parameters
----------
filenames : list of strings
Full paths to data files.
newParameters : dict
Contains the default parameters for the analysis.
verbose : bool, optional
False by default. If True, it will display a simple figure with the shape of the signal.
noPlot : bool, optional
False by default. If True it will disable the plotting
"""
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 = LoadData.OpenFile(filename, verbose=verbose)
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=Parameters['fittingMethod'], delay = Parameters['delay'])#, UseVoltageRange = [-0.4, 0.4])
if AllData == 0:
print('!!!! No Sweep in: ' + filename)
continue
if output['graphene']:
currents = ['i1', 'i2']
else:
currents = ['i1']
for current in currents:
Slope = AllData[current][CurveFit]['Slope']
Yintercept = AllData[current][CurveFit]['Yintercept']
if Type == 'Nanopore':
poreLength = Parameters['poreLength']
poresize = uf.CalculatePoreSize(np.abs(Slope), poreLength, specificConductance)
textstr = 'Nanopore Size\n\nSpecific Conductance: {}\nLength: {}\n\nConductance: {}\nDiameter: {}' \
.format(SpesCond.format_data(specificConductance), size.format_data(poreLength),
Cond.format_data(Slope),
size.format_data(poresize))
elif Type == 'Nanocapillary':
taperLength = Parameters['taperLength']
innerDiameter = Parameters['innerDiameter']
poresize = uf.CalculateCapillarySize(np.abs(Slope), innerDiameter, taperLength, specificConductance)
textstr = 'Nanocapillary Size\n\nSpecific Conductance: {}\nTaper lenghth {}:\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(poresize))
elif Type == 'NanocapillaryShrunken':
taperLength = Parameters['taperLength']
innerDiameter = Parameters['innerDiameter']
taperLengthShaft = Parameters['taperLengthShaft']
innerDiameterShaft = Parameters['innerDiameterShaft']
poresize = uf.CalculateShrunkenCapillarySize(np.abs(Slope), innerDiameter, taperLength, specificConductance,
taperLengthShaft, innerDiameterShaft)
textstr = 'Shrunken Nanocapillary Size\n\nSpecific Conductance: {}\nTaper length: {}\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(poresize))
if not noPlot:
figIV = plt.figure(2, figsize=(10, 7))
ax1IV = figIV.add_subplot(111)
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 ' + 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 + '_' + current + 'IV.pdf', transparent=True)
x = AllData[current]['Voltage'][ind]
y = AllData[current]['Mean'][ind]
csvfile = directory + os.sep + str(os.path.split(filename)[1]) + Type + '_' + current + '_IV.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()
#return poresize
#else:
#return poresize
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)
if (platform.system()=='Darwin'):
Tk().withdraw()
root=Tk()
root.update()

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