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Nanopore-tools/ObsoleteFunctions/ObsoleteFunctions.py
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ObsoleteFunctions.py
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import numpy as np
def SaveToHDF5(inp_file, AnalysisResults, coefficients, outdir):
file = str(os.path.split(inp_file['filename'])[1][:-4])
f = h5py.File(outdir + file + '_OriginalDB.hdf5', "w")
general = f.create_group("General")
general.create_dataset('FileName', data=inp_file['filename'])
general.create_dataset('Samplerate', data=inp_file['samplerate'])
general.create_dataset('Machine', data=inp_file['type'])
general.create_dataset('TransverseRecorded', data=inp_file['graphene'])
general.create_dataset('TimeFileWritten', data=inp_file['TimeFileWritten'])
general.create_dataset('TimeFileLastModified', data=inp_file['TimeFileLastModified'])
general.create_dataset('ExperimentDuration', data=inp_file['ExperimentDuration'])
segmentation_LP = f.create_group("LowPassSegmentation")
for k,l in AnalysisResults.items():
set1 = segmentation_LP.create_group(k)
lpset1 = set1.create_group('LowPassSettings')
for o, p in coefficients[k].items():
lpset1.create_dataset(o, data=p)
for m, l in AnalysisResults[k].items():
if m is 'AllEvents':
eventgroup = set1.create_group(m)
for i, val in enumerate(l):
eventgroup.create_dataset('{:09d}'.format(i), data=val)
elif m is 'Cusum':
eventgroup = set1.create_group(m)
for i1, val1 in enumerate(AnalysisResults[k]['Cusum']):
cusevent = eventgroup.create_group('{:09d}'.format(i1))
cusevent.create_dataset('NumberLevels', data=np.uint64(len(AnalysisResults[k]['Cusum'][i1]['levels'])))
if len(AnalysisResults[k]['Cusum'][i1]['levels']):
cusevent.create_dataset('up', data=AnalysisResults[k]['Cusum'][i1]['up'])
cusevent.create_dataset('down', data=AnalysisResults[k]['Cusum'][i1]['down'])
cusevent.create_dataset('both', data=AnalysisResults[k]['Cusum'][i1]['both'])
cusevent.create_dataset('fit', data=AnalysisResults[k]['Cusum'][i1]['fit'])
# 0: level number, 1: current, 2: length, 3: std
cusevent.create_dataset('levels_current', data=AnalysisResults[k]['Cusum'][i1]['levels'][1])
cusevent.create_dataset('levels_length', data=AnalysisResults[k]['Cusum'][i1]['levels'][2])
cusevent.create_dataset('levels_std', data=AnalysisResults[k]['Cusum'][i1]['levels'][3])
else:
set1.create_dataset(m, data=l)
def CorrelateTheTwoChannels(AnalysisResults, DelayLimit, Ch1 = 'i1', Ch2 = 'i2'):
if len(AnalysisResults[Ch1]['RoughEventLocations']) is not 0:
i1StartP = np.int64(AnalysisResults[Ch1]['StartPoints'][:])
else:
i1StartP = []
if len(AnalysisResults[Ch2]['RoughEventLocations']) is not 0:
i2StartP = np.int64(AnalysisResults[Ch2]['StartPoints'][:])
else:
i2StartP = []
# Common Events, # Take Longer
CommonEventsi1Index = np.array([], dtype=np.uint64)
CommonEventsi2Index = np.array([], dtype=np.uint64)
for k in i1StartP:
val = i2StartP[(i2StartP > k - DelayLimit) & (i2StartP < k + DelayLimit)]
if len(val) == 1:
CommonEventsi2Index = np.append(CommonEventsi2Index, np.uint64(np.where(i2StartP == val)[0][0]))
CommonEventsi1Index = np.append(CommonEventsi1Index, np.uint64(np.where(i1StartP == k)[0][0]))
if len(val) > 1:
diff = np.absolute(val-k)
CommonEventsi2Index = np.append(CommonEventsi2Index, np.uint64(np.where(i2StartP == val[np.argmin(diff)]))[0][0])
CommonEventsi1Index = np.append(CommonEventsi1Index, np.uint64(np.where(i1StartP == k)[0][0]))
# Only i1
Onlyi1Indexes = np.delete(range(len(i1StartP)), CommonEventsi1Index)
#Onlyi1Indexes=[]
# Only i2
Onlyi2Indexes = np.delete(range(len(i2StartP)), CommonEventsi2Index)
#Onlyi2Indexes=[]
CommonIndexes={}
CommonIndexes[Ch1]=CommonEventsi1Index
CommonIndexes[Ch2]=CommonEventsi2Index
OnlyIndexes={}
OnlyIndexes[Ch1] = Onlyi1Indexes
OnlyIndexes[Ch2] = Onlyi2Indexes
return (CommonIndexes, OnlyIndexes)
def PlotEvent(fig1, t1, i1, t2 = [], i2 = [], fit1 = np.array([]), fit2 = np.array([]), channel = 'i1'):
if len(t2)==0:
ax1 = fig1.add_subplot(111)
ax1.plot(t1, i1*1e9, 'b')
if len(fit1) is not 0:
ax1.plot(t1, fit1*1e9, 'y')
ax1.set_ylabel(channel + ' Current [nA]')
ax1.set_xlabel(channel + ' Time [s]')
ax1.ticklabel_format(useOffset=False)
ax1.ticklabel_format(useOffset=False)
return ax1
else:
ax1 = fig1.add_subplot(211)
ax2 = fig1.add_subplot(212, sharex=ax1)
ax1.plot(t1, i1*1e9, 'b')
if len(fit1) is not 0:
ax1.plot(t1, fit1*1e9, 'y')
ax2.plot(t2, i2*1e9, 'r')
if len(fit2) is not 0:
ax2.plot(t2, fit2*1e9, 'y')
ax1.set_ylabel('Ionic Current [nA]')
#ax1.set_xticklabels([])
ax2.set_ylabel('Transverse Current [nA]')
ax2.set_xlabel('Time [s]')
ax2.ticklabel_format(useOffset=False)
ax2.ticklabel_format(useOffset=False)
ax1.ticklabel_format(useOffset=False)
ax1.ticklabel_format(useOffset=False)
return ax1, ax2
def SaveAllPlots(CommonIndexes, OnlyIndexes, AnalysisResults, directory, out, buffer, withFit = 1):
if len(CommonIndexes['i1']) is not 0:
# Plot All Common Events
pp = PdfPages(directory + '_SavedEventsCommon.pdf')
ind1 = np.uint64(CommonIndexes['i1'])
ind2 = np.uint64(CommonIndexes['i2'])
t = np.arange(0, len(out['i1']))
t = t / out['samplerate'] * 1e3
count=1
for eventnumber in range(len(ind1)):
parttoplot = np.arange(AnalysisResults['i1']['StartPoints'][ind1[eventnumber]] - buffer,
AnalysisResults['i1']['EndPoints'][ind1[eventnumber]] + buffer, 1, dtype=np.uint64)
parttoplot2 = np.arange(AnalysisResults['i2']['StartPoints'][ind2[eventnumber]] - buffer,
AnalysisResults['i2']['EndPoints'][ind2[eventnumber]] + buffer, 1, dtype=np.uint64)
fit1 = np.concatenate([np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]],
np.ones(AnalysisResults['i1']['EndPoints'][ind1[eventnumber]] - AnalysisResults['i1']['StartPoints'][
ind1[eventnumber]]) * (
AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]] - AnalysisResults['i1']['DeltaI'][ind1[eventnumber]]),
np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]]])
fit2 = np.concatenate([np.ones(buffer) * AnalysisResults['i2']['LocalBaseline'][ind2[eventnumber]],
np.ones(AnalysisResults['i2']['EndPoints'][ind2[eventnumber]] - AnalysisResults['i2']['StartPoints'][
ind2[eventnumber]]) * (
AnalysisResults['i2']['LocalBaseline'][ind2[eventnumber]] - AnalysisResults['i2']['DeltaI'][ind2[eventnumber]]),
np.ones(buffer) * AnalysisResults['i2']['LocalBaseline'][ind2[eventnumber]]])
if withFit:
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], t[parttoplot2], out['i2'][parttoplot2],
fit1=fit1, fit2=fit2)
else:
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], t[parttoplot2], out['i2'][parttoplot2])
if not np.mod(eventnumber+1,200):
pp.close()
pp = PdfPages(directory + '_SavedEventsCommon_' + str(count) + '.pdf')
count+=1
pp.savefig(fig)
print('{} out of {} saved!'.format(str(eventnumber), str(len(ind1))))
print('Length i1: {}, Fit i1: {}'.format(len(out['i1'][parttoplot]), len(fit1)))
print('Length i2: {}, Fit i2: {}'.format(len(out['i2'][parttoplot2]), len(fit2)))
fig.clear()
plt.close(fig)
pp.close()
if len(OnlyIndexes['i1']) is not 0:
# Plot All i1
pp = PdfPages(directory + '_SavedEventsOnlyi1.pdf')
ind1 = np.uint64(OnlyIndexes['i1'])
t = np.arange(0, len(out['i1']))
t = t / out['samplerate'] * 1e3
count=1
for eventnumber in range(len(ind1)):
parttoplot = np.arange(AnalysisResults['i1']['StartPoints'][ind1[eventnumber]] - buffer,
AnalysisResults['i1']['EndPoints'][ind1[eventnumber]] + buffer, 1, dtype=np.uint64)
fit1 = np.concatenate([np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]],
np.ones(AnalysisResults['i1']['EndPoints'][ind1[eventnumber]] - AnalysisResults['i1']['StartPoints'][
ind1[eventnumber]]) * (
AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]] - AnalysisResults['i1']['DeltaI'][ind1[eventnumber]]),
np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][ind1[eventnumber]]])
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], t[parttoplot], out['i2'][parttoplot], fit1=fit1)
if not np.mod(eventnumber+1,200):
pp.close()
pp = PdfPages(directory + '_SavedEventsCommon_' + str(count) + '.pdf')
count+=1
pp.savefig(fig)
print('{} out of {} saved!'.format(str(eventnumber), str(len(ind1))))
fig.clear()
plt.close(fig)
pp.close()
if len(OnlyIndexes['i2']) is not 0:
# Plot All i2
pp = PdfPages(directory + '_SavedEventsOnlyi2.pdf')
ind1 = np.uint64(OnlyIndexes['i2'])
t = np.arange(0, len(out['i2']))
t = t / out['samplerate'] * 1e3
count=1
for eventnumber in range(len(ind1)):
parttoplot = np.arange(AnalysisResults['i2']['StartPoints'][ind1[eventnumber]] - buffer,
AnalysisResults['i2']['EndPoints'][ind1[eventnumber]] + buffer, 1, dtype=np.uint64)
fit1 = np.concatenate([np.ones(buffer) * AnalysisResults['i2']['LocalBaseline'][ind1[eventnumber]],
np.ones(AnalysisResults['i2']['EndPoints'][ind1[eventnumber]] - AnalysisResults['i2']['StartPoints'][
ind1[eventnumber]]) * (
AnalysisResults['i2']['LocalBaseline'][ind1[eventnumber]] - AnalysisResults['i2']['DeltaI'][ind1[eventnumber]]),
np.ones(buffer) * AnalysisResults['i2']['LocalBaseline'][ind1[eventnumber]]])
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], t[parttoplot], out['i2'][parttoplot], fit2=fit1)
if not np.mod(eventnumber+1,200):
pp.close()
pp = PdfPages(directory + '_SavedEventsCommon_' + str(count) + '.pdf')
count+=1
pp.savefig(fig)
print('{} out of {} saved!'.format(str(eventnumber), str(len(ind1))))
fig.clear()
plt.close(fig)
pp.close()
# Derivative
if len(CommonIndexes['i1']) is not 0:
# Plot All i1
pp = PdfPages(directory + '_i1vsderivi2.pdf')
ind1 = np.uint64(CommonIndexes['i1'])
ind2 = np.uint64(CommonIndexes['i2'])
t = np.arange(0, len(out['i1']))
t = t / out['samplerate'] * 1e3
count=1
for eventnumber in range(len(ind1)):
parttoplot = np.arange(AnalysisResults['i1']['StartPoints'][ind1[eventnumber]] - buffer,
AnalysisResults['i1']['EndPoints'][ind1[eventnumber]] + buffer, 1, dtype=np.uint64)
parttoplot2 = np.arange(AnalysisResults['i2']['StartPoints'][ind2[eventnumber]] - buffer,
AnalysisResults['i2']['EndPoints'][ind2[eventnumber]] + buffer, 1, dtype=np.uint64)
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], t[parttoplot2][:-1],
np.diff(out['i2'][parttoplot2]))
if not np.mod(eventnumber+1,200):
pp.close()
pp = PdfPages(directory + '_SavedEventsCommon_' + str(count) + '.pdf')
count+=1
pp.savefig(fig)
print('{} out of {} saved!'.format(str(eventnumber), str(len(ind1))))
fig.clear()
plt.close(fig)
pp.close()
def PlotRecursiveLPResults(RoughEventLocations, inp, directory, buffer, channel='i2'):
pp = PdfPages(directory + '_' + channel + '_DetectedEventsFromLPFilter.pdf')
a=1
for i in RoughEventLocations['RoughEventLocations']:
startp = np.uint64(i[0]-buffer*inp['samplerate'])
endp = np.uint64(i[1]+buffer*inp['samplerate'])
t = np.arange(startp, endp)
t = t / inp['samplerate'] * 1e3
fig = PlotEvent(t, inp[channel][startp:endp], channel=channel)
pp.savefig(fig)
print('{} out of {} saved!'.format(str(a), str(len(RoughEventLocations['RoughEventLocations']))))
a+=1
fig.clear()
plt.close(fig)
pp.close()
def SaveAllAxopatchEvents(AnalysisResults, directory, out, buffer, withFit = 1):
# Plot All Common Events
pp = PdfPages(directory + '_SavedEventsAxopatch.pdf')
t = np.arange(0, len(out['i1']))
t = t / out['samplerate'] * 1e3
for eventnumber in range(AnalysisResults['i1']['NumberOfEvents']):
parttoplot = np.arange(AnalysisResults['i1']['StartPoints'][eventnumber] - buffer,
AnalysisResults['i1']['EndPoints'][eventnumber] + buffer, 1, dtype=np.uint64)
fit1 = np.concatenate([np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][eventnumber],
np.ones(AnalysisResults['i1']['EndPoints'][eventnumber] -
AnalysisResults['i1']['StartPoints'][
eventnumber]) * (
AnalysisResults['i1']['LocalBaseline'][eventnumber] -
AnalysisResults['i1']['DeltaI'][eventnumber]),
np.ones(buffer) * AnalysisResults['i1']['LocalBaseline'][eventnumber]])
if withFit:
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot], fit1=fit1)
else:
fig = PlotEvent(t[parttoplot], out['i1'][parttoplot])
try:
pp.savefig(fig)
except:
print('Problem at {} !'.format(str(eventnumber)))
print('{} out of {} saved!'.format(str(eventnumber), str(AnalysisResults['i1']['NumberOfEvents'])))
#print('Length i1: {}, Fit i1: {}'.format(len(out['i1'][parttoplot]), len(fit1)))
fig.clear()
plt.close(fig)
pp.close()
def SetCusum2ARL0(deltax,sigmax,Arl0_2=1000,thresholdlevels=[1000,0.1,10]):
h0min=thresholdlevels[0];
h0max=thresholdlevels[1]; #detection threshold interval
ARL0=2*ARL0_2; #for two-sided algo
# Optimization on h "hopt"
change=0;
mu=deltax*(change-deltax/2)/sigmax**2;
sigma=abs(deltax)/sigmax;
mun=mu/sigma;
def f(h):
(exp(-2*mun*(h/sigma+1.166))-1+2*mun*(h/sigma+1.166))/(2*mun^2)-ARL0
if(f(h0min)*f(h0max)<0):
print('test')
#hopt=fzero(f,[h0min h0max])
elif(f(h0min) <0 and f(h0max) <0):
hopt=h0max
elif(f(h0min) >0 and f(h0max) >0):
hopt=h0min
hbook=sigmax*hopt/deltax;
return hbook, hopt
def event_detection(RawSignal, CusumParameters, RoughEventLocations, cutoff):
for i in range(len(RoughEventLocations)):
CusumReferencedEndPoint = RoughEventLocations[i][1] + CusumParameters['BaselineLength'];
CusumReferencedStartPoint = RoughEventLocations[i][0] - CusumParameters['BaselineLength'];
if CusumReferencedEndPoint > len(RawSignal):
CusumReferencedEndPoint = len(RawSignal)
if CusumReferencedStartPoint < 0:
CusumReferencedStartPoint = 0
if RoughEventLocations[i][2] < CusumParameters['ImpulsionLimit'] * CusumParameters['SamplingFrequency']:
trace = RawSignal[CusumReferencedStartPoint:CusumReferencedEndPoint]
#[mc,krmv]=ImpulsionFitting(trace,BaselineLength, cutoff, SamplingFrequency);
#EventType='Impulsion';
#krmv=[BaselineLength, BaselineLength+RoughEventLocations(i,3)];
#mc=[ones(1,BaselineLength+1)*mean(trace(1:BaselineLength)), ones(1,krmv(2)-krmv(1)-1)*min(trace), ones(1,BaselineLength-2)*mean(trace(krmv(2):end))];
else:
mc, kd, krmv = cusum(RawSignal[CusumReferencedStartPoint:CusumReferencedEndPoint],CusumParameters['delta'],CusumParameters['h'])
EventType='Standard Event';
Startpoint = CusumReferencedStartPoint + krmv[0]
EndPoint = CusumReferencedStartPoint + krm[-1]
BaselinePart = RawSignal[CusumReferencedStartPoint:CusumReferencedStartPoint]
def EredoxBefore14062018():
Eredox = np.array([31.7, 82.9, 135, 185], dtype=float)
Eredox = Eredox * 1e-3
return (Eredox-Eredox[0])
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