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Nanopore-tools/Plotting/Stability Plots.py
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Stability Plots.py
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import platform
from sys import platform as sys_pf
if sys_pf == 'darwin':
import matplotlib
matplotlib.use("TkAgg")
import matplotlib
import numpy as np
import scipy
from scipy.optimize import curve_fit
from scipy import constants as cst
import Functions as uf
import os
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import h5py
import pandas as pd
from matplotlib.ticker import EngFormatter
from matplotlib import rc
import LoadData
#rc('text', usetex=True)
from tkinter import Tk
from tkinter.filedialog import askopenfilenames
import seaborn as sns
from matplotlib import gridspec
import os
import platform
import os, time
# np.seterr(divide='ignore', invalid='ignore')
root = Tk()
root.withdraw()
#Set units formatting
from matplotlib.ticker import EngFormatter
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
formCurrent = EngFormatter(unit='A', places=3)
formA = EngFormatter(unit='A', places=3)
formB = EngFormatter(unit='s', places=3)
filenames = askopenfilenames()
root.update()
time_array_long = []
current_array_long = []
voltage_array_long = []
conductance_array_long = []
last_el = 0
for i, file in enumerate(filenames):
dat = LoadData.OpenFile(file)
fig1 = plt.figure(1, figsize=(8, 4))
ax_part1 = fig1.add_subplot(2, 1, 1)
#time data
time_array = np.arange(len(dat['i1']))/dat['samplerate']
#Ionic current
current_array = np.array(dat['i1'] * 1e9)
current_array_long = np.append([current_array_long],[[current_array]])
# #Conductance (G)
G = dat['i1']/dat['v1']*1e9
conductance_array = np.array(G)
conductance_array_long = np.append([conductance_array_long],[[conductance_array]])
#Voltage
voltage_array = np.array(len(dat['v1'] * 1e3))
voltage_array_long = np.append([voltage_array_long], [[voltage_array]])
#fix the time after joining
time_interval = time_array[1] - time_array[0]
time_array_long = np.concatenate((time_array_long, time_array+last_el+time_interval))
last_el = time_array_long[-1]
fig2 = plt.figure(1, figsize=(8, 4))
ax_part2 = fig2.add_subplot(2, 1, 2, sharex=ax_part1)
time_array_long -= time_interval
# clean_data = np.where(
# ((time_array_long < 5) & (time_array_long > 0))|
# ((time_array_long < 15) & (time_array_long > 10))
# )
# # time_array_long[clean_data] = np.NaN #specify ranges that are masked and not plotted
# time_array_long [int(3e5):int(5e5)] = np.NaN
# time_array_long [int(7e5):int(9e5)] = np.NaN
# time_array_long [int(11e5):int(13e5)] = np.NaN
# time_array_long [int(15e5):int(17e5)] = np.NaN
# time_array_long [int(19e5):int(21e5)] = np.NaN
# time_array_long [int(23e5):int(25e5)] = np.NaN
# time_array_long [int(27e5):int(29e5)] = np.NaN
# time_array_long [int(31e5):int(33e5)] = np.NaN
# time_array_long [int(35e5):int(37e5)] = np.NaN
print(len(time_array_long),
len(current_array_long),
len(voltage_array_long),
len(conductance_array_long))
print('Done')
ax_part1.plot(time_array_long[::], conductance_array_long [::])
ax_part2.plot(time_array_long[::], current_array_long[::])
plt.xlabel ('Time(s)')
# plt.ylabel ('Ionic current (nA)')
#plt.savefig("joy25p67m_stability_plot.svg")
# plt.savefig( "joy25p67m_stability_plot.png")
plt.show()
root.update()
# print("last modified: %s" % time.ctime(os.path.getmtime(file)))
# print("created: %s" % time.ctime(os.path.getctime(file)))
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