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Nanopore-tools/Plotting/MultipleIVs.py
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MultipleIVs.py
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# -*- coding: utf-8 -*-
from sys import platform as sys_pf
import matplotlib
from sys import platform as sys_pf
if sys_pf == 'darwin':
import matplotlib
matplotlib.use("TKAgg")
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': 21, # 10.5 S/m for 1M KCl
'delay': 5, # seconds for reading current
# Nanopore
'poreLength': 1e-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:")
print(Parameters)
def run(filenames, newParameters={}, verbose=False, noPlot=False):
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 = [-0.51, 0.51])
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)
if not noPlot:
figIV = plt.figure(2, figsize=(10, 7))
ax1IV = figIV.add_subplot(111)
ind = np.argsort(AllData[current]['Voltage'])
ax1IV.errorbar(AllData[current]['Voltage'][ind], AllData[current]['Mean'][ind],
yerr=AllData[current]['SE'][ind], fmt='o')
ax1IV.plot(AllData[current]['Voltage'][ind], np.polyval([Slope, Yintercept], AllData[current]['Voltage'][ind]), label=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.legend()
ax1IV.xaxis.set_major_formatter(EngFormatter(unit='V'))
ax1IV.yaxis.set_major_formatter(EngFormatter(unit='A'))
# ax1IV.set_xlim(-0.6, 0.6)
# ax1IV.set_ylim(-15e-9, 15e-9)
ax1IV.grid(True)
figIV.savefig(directory + os.sep + str(os.path.split(filename)[1]) + Type + '_' + current + 'IV.pdf',
transparent=True)
plt.show()
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.destroy()
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