def testSaving2(self):
channel = "C4-A1"
fpath = parentdir #u'C:/DATA/Vickie_spindles/'
fileName = "/test.bdf" #'PETCHn1.bdf'
AmpEventName = 'SpindleAmp'
detectionStages = ["Sleep stage 2", "Sleep stage N2"]
#print "Converting .sig file to .bdf file..."
#readerSIG = HarmonieReader(fpath + 'PETCHn1.SIG')
#readerSIG.saveAsEDF(fpath + fileName, "BDF", verbose=False)
reader1 = EDFReader(fpath + fileName)
# Delete any present event with the name AmpEventName
reader1.events = [e for e in reader1.events if e.name != AmpEventName]
detector = SpindleDectectorAmp(reader1, usePickled=False)
detector.setDetectionStages(detectionStages)
detector.detectSpindles(channelList=[channel])
detector.saveSpindle(reader1, AmpEventName, "Spindle")
reader2 = EDFReader(fpath + fileName)
events1 = [
e for e in reader1.events
if e.name == AmpEventName and e.channel == channel
]
events2 = [
e for e in reader2.events
if e.name == AmpEventName and e.channel == channel
]
for event1, event2 in zip(events1, events2):
self.assertEqual(event1, event2)
def testLoadSaveLoad(self):
fpath = parentdir #u'C:/DATA/Vickie_spindles/'
fileName = "/test.bdf" #'PETCHn1.bdf'
print("Converting .sig file to .bdf file...")
readerSIG = HarmonieReader(fpath + fileName[:-3] + 'SIG')
readerSIG.saveAsEDF(fpath + fileName, "BDF", verbose=False)
reader = EDFReader(fpath + fileName)
reader.saveAs(fpath + "temp.bdf")
del reader
with io.open(fpath + fileName, 'rb') as file1:
with io.open(fpath + "temp.bdf", 'rb') as file2:
while 1:
bytes1 = file1.read(100)
bytes2 = file2.read(100)
if not bytes1:
break
self.assertEqual(bytes1, bytes2)
os.remove(fpath + "temp.bdf")
def testConversion_readChannel(self):
#loadFiles()
print("Reading the .sig file...")
readerSIG = HarmonieReader(os.path.join(parentdir, "test.SIG"))
print("Saving a copy in the BDF format...")
readerSIG.saveAsEDF(os.path.join(parentdir, "test.bdf"),
"BDF",
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
print("Reading the saved BDF file...")
readerEDF = EDFReader(os.path.join(parentdir, "test.bdf"),
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
channelListSig = readerSIG.getChannelLabels()
channelListEdf = readerEDF.getChannelLabels()
for channelSig, channelEdf in zip(channelListSig, channelListEdf):
data1 = readerSIG.readChannel(channelSig, False)
Y1 = data1.signal
T1 = readerSIG.getChannelTime(channelSig)
#fsSIG = data.samplingRate
data2 = readerEDF.readChannel(channelEdf)
Y2 = data2.signal
T2 = readerEDF.getChannelTime(channelEdf)
#fsEDF = data.samplingRate
print(("1:", np.mean(abs(Y1)), np.mean(abs(Y2))))
def testConversion(self):
#loadFiles()
readerSIG = HarmonieReader(os.path.join(parentdir, "test.SIG"))
print("Saving a copy in the BDF format...")
readerSIG.saveAsEDF(os.path.join(parentdir, "test.bdf"),
"BDF",
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
print("Reading the saved BDF file...")
readerEDF = EDFReader(os.path.join(parentdir, "test.BDF"),
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
channelListSig = readerSIG.getChannelLabels()
channelListEdf = readerEDF.getChannelLabels()
# For each pages, verify that the signals in reader and readerEDF
# are essentially the same by verifying their signal-to-noise ratio
for noPage in range(readerSIG.getNbRecords()):
# We test only complete pages since incomplete pages will be
# different for the two formats, the EDF format padding zeros
# at the end of the page to make complete records.
if readerSIG.getInfoRecords(noPage + 1).isComplete:
pageSIG = readerSIG.readRecord(channelListSig, noPage + 1)
pageEDF = readerEDF.readRecord(channelListEdf, noPage + 1)
for channelSig, channelEdf in zip(channelListSig,
channelListEdf):
Y1 = pageSIG.getSignal(channelSig)
Y2 = pageEDF.getSignal(channelEdf)
SNR = 10.0 * log10(trapz(Y1**2) / trapz((Y1 - Y2)**2))
print(("noPage=", noPage + 1, "(of ",
readerSIG.getNbRecords(), ")", "channel=",
channelSig, "SNR=", SNR))
if channelSig != "Mic-Mic" and SNR < 50.0:
import pylab
pylab.plot(list(range(len(Y1))), Y1)
pylab.plot(list(range(len(Y2))), Y2)
pylab.show()
self.failIf(channelSig != "Mic-Mic" and SNR < 50.0)
else:
print(("Skiping incomplete page " + str(noPage + 1)))
def testSaving1(self):
print("Converting .sig file to .bdf file...")
readerSIG = HarmonieReader(parentdir + "/test.SIG")
readerSIG.saveAsEDF(parentdir + "/test.BDF", "BDF", verbose=False)
print("Reading the .bdf file...")
reader = EDFReader(parentdir + "/test.BDF")
detectionStages = ["Sleep stage N2", "Sleep stage 2"]
channelList = ['F3-A1', 'F4-A1']
detector = SpindleDectectorAmp(reader, usePickled=False)
detector.setDetectionStages(detectionStages)
detector.detectSpindles(channelList=channelList)
nbEvents = len(reader.events) + len(detector.detectedSpindles)
detector.saveSpindle(reader, "SpindleRMS", "Spindle")
reader2 = EDFReader(parentdir + "/test.BDF")
self.failIf(nbEvents != len(reader2.events))
evaluator = DetectorEvaluator()
evaluator.computeStatistics(detectionStages, "SpindleRMS",
"SpindleRMS", reader, reader2, channelList)
for channel in channelList:
try:
self.assertEqual(evaluator.sensitivity(channel), 1.0)
self.assertEqual(evaluator.specificity(channel), 1.0)
self.assertEqual(evaluator.PPV(channel), 1.0)
self.assertEqual(evaluator.NPV(channel), 1.0)
except AssertionError:
print("channel=",
channel,
"; sensitivity=",
evaluator.sensitivity(channel),
end=' ')
print("; specificity=",
evaluator.specificity(channel),
"; PPV=",
end=' ')
print(evaluator.PPV(channel), "; NPV=", evaluator.NPV(channel))
raise
def testDoubleDetection(self):
AmpEventName = 'SpindleAmp'
RMSEventName = 'SpindleRMS'
fpath = parentdir #u'C:/DATA/Vickie_spindles/'
fileName = "/test.bdf" #'PETCHn1.bdf'
detectionStages = ["Sleep stage 2", "Sleep stage N2"]
channels = ["C4-A1"]
print("Converting .sig file to .bdf file...")
readerSIG = HarmonieReader(fpath + fileName[:-3] + 'SIG')
readerSIG.saveAsEDF(fpath + fileName, "BDF", verbose=False)
reader = EDFReader(fpath + fileName)
# Delete any present event with the name AmpEventName
#reader.events = [e for e in reader.events if e.name != AmpEventName]
#reader.events = [e for e in reader.events if e.name != RMSEventName]
detector = SpindleDectectorAmp(reader, usePickled=False)
detector.quantileThreshold = 0.925
detector.setDetectionStages(detectionStages)
detector.computeRMS = False
detector.computeFreq = False
detector.computeSlopeFreq = False
detector.detectSpindles(channelList=channels)
nbSpins1 = len(detector.detectedSpindles)
detector.saveSpindle(reader, AmpEventName, "Spindle")
detector.detectSpindles(channelList=channels)
nbSpins2 = len(detector.detectedSpindles)
detector.saveSpindle(reader, RMSEventName, "Spindle")
try:
self.assertEqual(nbSpins1, nbSpins2)
except AssertionError:
print(nbSpins1, nbSpins2)
raise
evaluatorAmp = DetectorEvaluator()
evaluatorAmp.computeStatistics(detectionStages,
RMSEventName,
AmpEventName,
reader,
channelList=channels)
for channel in channels:
if channel in evaluatorAmp.TP:
self.assertEqual(evaluatorAmp.sensitivity(channel), 1.0)
self.assertEqual(evaluatorAmp.specificity(channel), 1.0)
self.assertEqual(evaluatorAmp.PPV(channel), 1.0)
self.assertEqual(evaluatorAmp.NPV(channel), 1.0)
def testDoubleDetection(self):
fpath = parentdir #u'C:/DATA/Vickie_spindles/'
fileName = "/test.bdf" #'PETCHn1.bdf'
channels = ["C4-A1"]
print("Converting .sig file to .bdf file...")
readerSIG = HarmonieReader(fpath + fileName[:-3] + 'SIG')
readerSIG.saveAsEDF(fpath + fileName, "BDF", verbose=False)
reader = EDFReader(fpath + fileName)
data = reader.readChannel(channels[0], usePickled=False)
signal = data.signal
print(signal[[1, 100, 200, 300, 400, 500]])
data = reader.readChannel(channels[0], usePickled=False)
signal = data.signal
print(signal[[1, 100, 200, 300, 400, 500]])
def testLoadDetectSaveLoad(self):
fpath = parentdir #u'C:/DATA/Vickie_spindles/'
fileName = "/test.bdf" #'PETCHn1.bdf'
AmpEventName = 'SpindleAmp'
RMSEventName = 'SpindleRMS'
detectionStages = ["Sleep stage 2", "Sleep stage N2"]
channels = ["C4-A1"]
print("Converting .sig file to .bdf file...")
readerSIG = HarmonieReader(fpath + fileName[:-3] + 'SIG')
readerSIG.saveAsEDF(fpath + fileName, "BDF", verbose=False)
reader = EDFReader(fpath + fileName)
# Delete any present event with the name AmpEventName
reader.events = [e for e in reader.events if e.name != AmpEventName]
reader.events = [e for e in reader.events if e.name != RMSEventName]
detector = SpindleDectectorAmp(reader, usePickled=False)
detector.quantileThreshold = 0.925
detector.setDetectionStages(detectionStages)
detector.computeRMS = False
detector.computeFreq = False
detector.computeSlopeFreq = False
detector.detectSpindles(channelList=channels)
detector.saveSpindle(reader, AmpEventName, "Spindle")
copyfile(fpath + fileName, fpath + "temp.bdf")
reader = EDFReader(fpath + fileName)
# Delete any present event with the name AmpEventName
reader.events = [e for e in reader.events if e.name != AmpEventName]
reader.events = [e for e in reader.events if e.name != RMSEventName]
detector = SpindleDectectorAmp(reader, usePickled=False)
detector.quantileThreshold = 0.925
detector.setDetectionStages(detectionStages)
detector.computeRMS = False
detector.computeFreq = False
detector.computeSlopeFreq = False
detector.detectSpindles(channelList=channels)
detector.saveSpindle(reader, AmpEventName, "Spindle")
with io.open(fpath + fileName, 'rb') as file1:
with io.open(fpath + "temp.bdf", 'rb') as file2:
byte1 = file1.read(1)
byte2 = file2.read(1)
self.assertEqual(byte1, byte2)
os.remove(fpath + "temp.bdf")