Homec4science
Diffusion Nanopore Tools (smalladditions) Browse

Nanopore-tools/EventDetectionJD.py
31eb273b9a5bsmalladditions

Last Change
Raw File

EventDetectionJD.py
View Options

import NanoporeClasses as NC
import shelve
import os
import glob
from time import sleep
import Functions
from pprint import pprint
def batcheventdetection(folder,extension,coefficients):
AllEvents=NC.AllEvents()
for fullfilename in glob.glob(os.path.join(folder,extension)):
print('analysing '+fullfilename)
filename, file_extension = os.path.splitext(fullfilename)
savefilename=filename+'data'
tEL=eventdetection(fullfilename,coefficients)
shelfFile=shelve.open(savefilename)
shelfFile['translocationEvents']=tEL
#tEL=shelfFile['translocationEvents']
pprint('found {} events'.format(len(tEL.events)))
shelfFile.close()
AllEvents.AddEvent(tEL)
return AllEvents
def eventdetection(fullfilename,coefficients,showFigures = False):
loadedData=Functions.OpenFile(fullfilename)
#pprint(loadedData)
minTime=coefficients['minEventLength']
print('eventdetection...', end='')
events=Functions.RecursiveLowPassFast(loadedData['i1'],coefficients,loadedData['samplerate'])
# print('nr events: {}'.format(len(events)))
translocationEventList=NC.AllEvents()
if showFigures:
plt.figure(1)
plt.cla()
timeVals=np.linspace(0, len(loadedData['i1'])/loadedData['samplerate'], num=len(loadedData['i1']))
plt.plot(timeVals,loadedData['i1'])
plt.draw()
plt.pause(0.001)
# for i in range(length(events)):
#print('min ticks:{}'.format(minTime*loadedData['samplerate']))
for i in range((len(events))):
beginEvent=events[i][0]
endEvent=events[i][1]
meanEvent=events[i][2]
stdEvent=events[i][3]
if (endEvent-beginEvent)>=(minTime*loadedData['samplerate']) and (endEvent-beginEvent)<(coefficients['eventlengthLimit']*loadedData['samplerate']):
newEvent=NC.TranslocationEvent(fullfilename)
Trace=loadedData['i1'][int(beginEvent):int(endEvent)]
traceBefore=loadedData['i1'][int(beginEvent)-100:int(beginEvent)-1]
traceAfter=loadedData['i1'][int(endEvent)+1:int(endEvent)+100]
newEvent.SetEvent(Trace,meanEvent,loadedData['samplerate'])
newEvent.SetCoefficients(coefficients)
newEvent.SetBaselineTrace(traceBefore,traceAfter)
translocationEventList.AddEvent(newEvent)
if showFigures:
minVal=np.max(loadedData['i1'])#-1.05e-9 #np.min(loadedData['i1'])
maxVal=np.max(loadedData['i1'])+0.05e-9#-1.05e-9 #np.min(loadedData['i1'])
for i in range(len(newEvents)):
beginEvent=newEvents[i][0]
plt.plot([beginEvent/loadedData['samplerate'], beginEvent/loadedData['samplerate']], [minVal, maxVal], 'y-', lw=1)
plt.draw()
plt.pause(0.001)
return translocationEventList
def LoadEvents(folder):
savefile=os.path.join(folder,os.path.basename(folder)+'_Events')
shelfFile=shelve.open(savefile)
TranslocationEvents=shelfFile['TranslocationEvents']
shelfFile.close()
AllEvents=NC.AllEvents()
AllEvents.AddEvent(TranslocationEvents)
return AllEvents
c4science · Help