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Nanopore-tools/NanoporeClasses.py
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NanoporeClasses.py
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import numpy as np
from pprint import pprint
import shelve
import os
import math
from Plotting.NanoporePlots import PlotCurrentTrace,PlotCurrentTraceBaseline
import matplotlib.pyplot as plt
from matplotlib.ticker import EngFormatter
Amp = EngFormatter(unit='A', places=2)
Time = EngFormatter(unit='s', places=2)
Volt = EngFormatter(unit='V', places=2)
class TranslocationEvent:
def __init__(self, filename):
self.filename = filename
def SetEvent(self,eventTrace,baseline,samplerate):
self.eventTrace=eventTrace
self.baseline=baseline
self.samplerate=samplerate
self.meanTrace=np.mean(eventTrace)
self.lengthEvents=len(eventTrace)/samplerate
self.currentDrop=baseline-np.mean(eventTrace)
def SetCoefficients(self,coefficients):
self.coefficients=coefficients
def SetBaselineTrace(self, before,after):
self.before=before
self.after=after
def PlotEvent(self):
part1=np.append(self.before,self.eventTrace)
fn=filename_w_ext = os.path.basename(self.filename)
plotTitle = fn + '\n' + 'Event length: {}\nCurrent drop: {}'.format(Time.format_data(self.lengthEvents), Amp.format_data(self.currentDrop))
#PlotCurrentTraceBaseline(self.before, self.eventTrace, self.after, self.samplerate, titleplot)
timeVals1 = np.linspace(0, len(self.before) / self.samplerate, num=len(self.before))
timeVals2 = np.linspace(0 + max(timeVals1), len(self.eventTrace) / self.samplerate + max(timeVals1),
num=len(self.eventTrace))
timeVals3 = np.linspace(0 + max(timeVals2), len(self.after) / self.samplerate + max(timeVals2), num=len(self.after))
# plt.figure(figsize=(10, 6))
fig, ax = plt.subplots(figsize=(10, 6))
ax.plot(timeVals1, self.before, color='tomato')
ax.plot(timeVals2, self.eventTrace, color='mediumslateblue')
ax.plot(timeVals3, self.after, color='tomato')
beforeBaseline=np.full(len(self.before), self.baseline)
ax.plot(timeVals1,beforeBaseline, '--', color='tomato')
afterBaseline = np.full(len(self.after), self.baseline)
ax.plot(timeVals3,afterBaseline, '--', color='tomato')
meanTrace = np.full(len(self.eventTrace), self.meanTrace)
ax.plot(timeVals2,meanTrace, '--', color='mediumslateblue')
ax.set_xlabel('time (s)')
ax.set_ylabel('current (A)')
ax.xaxis.set_major_formatter(Time)
ax.yaxis.set_major_formatter(Amp)
if plotTitle:
plt.title(plotTitle)
plt.show()
class AllEvents:
def __init__(self):
self.events=[]
def AddEvent(self, translocationEvent):
if isinstance(translocationEvent,AllEvents):
self.events.extend(translocationEvent.events)
elif isinstance(translocationEvent,list):
self.events.extend(translocationEvent)
else:
self.events.append(translocationEvent)
def GetAllLengths(self):
Lengths=[event.lengthEvents for event in self.events]
return Lengths
def GetAllIdrops(self):
currentDrops=[event.currentDrop for event in self.events]
return currentDrops
def GetAllIdropsNorm(self):
currentDrops = [event.currentDrop/ event.baseline for event in self.events]
return currentDrops
def SaveEvents(self,savename):
if os.path.isdir(savename):
savefile=os.path.join(savename,os.path.basename(savename)+'_Events')
else:
if os.path.isfile(savename + '.dat'):
raise IOError('File ' + savename + '.dat already exists.')
else:
savefile = savename
#Check if directory exists
directory = os.path.dirname(savefile)
if not os.path.exists(directory):
os.makedirs(directory)
shelfFile=shelve.open(savefile)
shelfFile['TranslocationEvents']=self.events
shelfFile.close()
print('saved as: ' + savefile + '.dat')
# if os.path.exists(savefile + '.bak'):
# os.remove(savefile + '.bak')
# if os.path.exists(savefile + '.dir'):
# os.remove(savefile + '.dir')
def GetEventsMinCondition(self,minCurrent=-math.inf,maxCurrent=math.inf,minLength=0,maxLength=math.inf):
minCurrent = -math.inf if not minCurrent else minCurrent
maxCurrent = math.inf if not maxCurrent else maxCurrent
minLength = 0 if not minLength else minLength
maxLength = math.inf if not maxLength else maxLength
newEvents=AllEvents()
for event in self.events:
if minCurrent<event.currentDrop<maxCurrent and minLength<event.lengthEvents<maxLength:
newEvents.AddEvent(event)
print('selected {} events from {}'.format(len(newEvents.events), len(self.events)))
return newEvents
def PlotAllEvents(self):
for event in self.events:
event.PlotEvent()
def PlotIEvent(self,i):
event=self.events[i]
event.Plotevent()
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