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Nanopore-tools/Plotting/PlotFile2Channels.py
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PlotFile2Channels.py
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import UsefulFunctions as uf
import pyqtgraph as pg
import matplotlib.pyplot as plt
from timeit import default_timer as timer
import scipy
import numpy as np
import os
import matplotlib
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.font_manager import FontProperties
from tkinter import Tk
from tkinter.filedialog import askopenfilenames
from matplotlib.ticker import EngFormatter
matplotlib.rcParams['agg.path.chunksize'] = 100000
fontP = FontProperties()
fontP.set_size('small')
props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
Tk().withdraw()
os.system('''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' ''')
#filenames = ['/Volumes/backup/2017/Michael/Axopatch/20170512/10mMKClInFlowCellORingPore1mm.dat']
filenames = ['/Volumes/lben-archives/2016/Michael/Axopatch/21112016/17B_100mMCis1MtransKCl_80mer_9.dat']
expname = 'All'
#filenames = askopenfilenames() # show an "Open" dialog box and return the path to the selected file
#filenames={'/Users/migraf/Desktop/22B_UpperRibbonOverNight_.dat'}
#With Voltages
volt = 1
for filename in filenames:
print(filename)
out = uf.ImportAxopatchData(filename)
fig = plt.figure(1, figsize=(8.7,5.96) )
if volt:
ax = fig.add_subplot(311)
ax2 = fig.add_subplot(312, sharex = ax)
ax3 = fig.add_subplot(313, sharex = ax)
ax3.yaxis.set_major_formatter(EngFormatter(unit='V'))
ax3.set_ylabel('Voltage')
else:
ax = fig.add_subplot(211)
ax2 = fig.add_subplot(212, sharex = ax)
ax.plot(np.arange(0, len(out['i1']))/out['samplerate'], out['i1'], 'b')
ax2.plot(np.arange(0, len(out['i2']))/out['samplerate'], out['i2'], 'r')
if volt:
ax3.plot(np.arange(0, len(out['i1']))/out['samplerate'], out['v1'], 'b')
ax3.plot(np.arange(0, len(out['i1'])) / out['samplerate'], out['v2'], 'r')
#ax.set_xlim(41000, 42600)
#ax2.set_xlim(41000, 42600)
#ax.set_ylim(-5,15)
ax.set_xlabel('Time')
ax2.set_xlabel('Time')
ax.set_ylabel('Ionic Current')
ax2.set_ylabel('Transverse Current')
ax.xaxis.set_major_formatter(EngFormatter(unit='s'))
ax.yaxis.set_major_formatter(EngFormatter(unit='A'))
ax2.yaxis.set_major_formatter(EngFormatter(unit='A'))
#fig1.savefig(filename[:-4] + '.png', dpi=300)
plt.show()
#fig1.clear()
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