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Merge pull request #103 from catalystneuro/event-detector-changes
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audio event detector working even if no microphone data is present
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@luiztauffer
luiztauffer authored Jul 1, 2020
2 parents 4f26fe2 + 94b8d8c commit e7365c3
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Showing 2 changed files with 46 additions and 56 deletions.
7 changes: 2 additions & 5 deletions ecogvis/ecogvis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -622,11 +622,8 @@ def audio_event_detection(self):
# Test if trials already exist
if 'TimeIntervals_speaker' not in self.model.nwb.intervals:
# Test if file contains audio signals
# if ('microphone' in self.model.nwb.acquisition) and ('speaker1' in self.model.nwb.stimulus):
if any(name in self.model.nwb.acquisition for name in ['anin4', 'microphone']) and ('speaker1' in self.model.nwb.stimulus):
w = AudioEventDetection(parent=self)
if w.value == 1: # Trial times were detected
self.model.refresh_file() # re-opens the file, now with new data
if any(name in self.model.nwb.stimulus for name in ['speaker1', 'speaker2']):
AudioEventDetection(parent=self)
else:
NoAudioDialog()
else:
Expand Down
95 changes: 44 additions & 51 deletions ecogvis/functions/audio_event_detection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,19 +185,22 @@ def reset_draw(self):
self.source_stim = self.stimuli[stim]
self.signal_stim = self.source_stim.data
self.stimTimes = [] # clears any previous stim times
self.signal_stim_filt = None # clears any previous smoothed speaker
self.signal_stim_filt = None # clears any previous smoothed speaker

# Response variables
resp = self.combo1.currentText()
self.source_resp = self.responses[resp]
self.signal_resp = self.source_resp.data
self.respTimes = [] # clears any previous resp times
self.source_resp = None
self.signal_resp = None
self.signal_resp_filt = None
self.respTimes = [] # clears any previous resp times
if resp in self.responses:
self.source_resp = self.responses[resp]
self.signal_resp = self.source_resp.data

# Common to both stim and resp
self.fs = self.source_stim.rate
self.nTotalBins = self.signal_stim.shape[0]
self.timeaxis = np.arange(self.nTotalBins)/self.fs
self.timeaxis = np.arange(self.nTotalBins) / self.fs
self.maxTime = self.timeaxis[-1]
self.draw_scene()

Expand Down Expand Up @@ -253,8 +256,7 @@ def draw_scene(self):
# self.win.addLegend()

# Plot stimuli
plotBins = np.logical_and(self.timeaxis>=self.startTime,
self.timeaxis<=self.stopTime)
plotBins = np.logical_and(self.timeaxis >= self.startTime, self.timeaxis <= self.stopTime)
x = self.timeaxis[plotBins]
y0 = self.signal_stim[plotBins].astype(float)
y0 /= np.max(np.abs(y0))
Expand All @@ -263,53 +265,49 @@ def draw_scene(self):
name='Speaker')

# Plot responses
y1 = self.signal_resp[plotBins].astype(float)
y1 /= np.max(np.abs(y1))
self.win.plot(x, y1 + self.mic_offset,
pen=pg.mkPen(self.red_light, width=1.), name='Mic')

if self.signal_stim_filt is not None \
and self.signal_resp_filt is not None:

plotBinsFilt = np.logical_and(self.timeaxis_filt>=self.startTime,
self.timeaxis_filt<=self.stopTime)
if self.signal_resp is not None:
y1 = self.signal_resp[plotBins].astype(float)
y1 /= np.max(np.abs(y1))
self.win.plot(x, y1 + self.mic_offset, pen=pg.mkPen(self.red_light, width=1.), name='Mic')

if self.signal_stim_filt is not None:
plotBinsFilt = np.logical_and(self.timeaxis_filt >= self.startTime,
self.timeaxis_filt <= self.stopTime)
x_filt = self.timeaxis_filt[plotBinsFilt]

# Plot filtered stimulus and threshold
y0 = [self.signal_stim_filt[plotBinsFilt],
np.ones(np.sum(plotBinsFilt)) * self.speakerThresh]
y0_names = ['SpeakerFilt', 'SpeakerThresh']
y0_kargs = [{'color': self.gray, 'width': 2.},
{
'color': self.blue, 'width': 1.5,
'style': QtCore.Qt.DashLine
}]
y0_kargs = [
{'color': self.gray, 'width': 2.},
{'color': self.blue, 'width': 1.5, 'style': QtCore.Qt.DashLine}
]
for name, kargs, column in zip(y0_names, y0_kargs, y0):
self.win.plot(x_filt, column + self.speaker_offset,
pen=pg.mkPen(**kargs), name=name)

for st in self.stimTimes:
if st>self.startTime and st<=self.stopTime:
if st > self.startTime and st <= self.stopTime:
self.win.plot([st, st], self.ylim,
pen=pg.mkPen(self.blue, width=2.))

if self.signal_resp_filt is not None:
# Plot filtered response and threshold
y1 = [self.signal_resp_filt[plotBinsFilt],
np.ones(np.sum(plotBinsFilt)) * self.micThresh]
y1_names = ['MicFilt', 'MicThresh']
y1_kargs = [{'color': self.gray, 'width': 2.},
{
'color': self.red, 'width': 1.5,
'style': QtCore.Qt.DashLine
}]
for name, kargs, column in zip(y1_names, y1_kargs, y1):
self.win.plot(x_filt, column + self.mic_offset,
pen=pg.mkPen(**kargs), name=name)
if self.signal_resp_filt is not None:
y1 = [self.signal_resp_filt[plotBinsFilt], np.ones(np.sum(plotBinsFilt)) * self.micThresh]
y1_names = ['MicFilt', 'MicThresh']
y1_kargs = [
{'color': self.gray, 'width': 2.},
{'color': self.red, 'width': 1.5, 'style': QtCore.Qt.DashLine}
]
for name, kargs, column in zip(y1_names, y1_kargs, y1):
self.win.plot(x_filt, column + self.mic_offset,
pen=pg.mkPen(**kargs), name=name)

for rt in self.respTimes:
if rt>self.startTime and rt<=self.stopTime:
self.win.plot([rt, rt], self.ylim,
pen=pg.mkPen(self.red, width=2.))
if rt > self.startTime and rt <= self.stopTime:
self.win.plot([rt, rt], self.ylim, pen=pg.mkPen(self.red, width=2.))

# Axes parameters
self.win.setXRange(self.startTime, self.stopTime)
Expand All @@ -330,8 +328,7 @@ def run_test(self):
# from the interval plotted.
self.set_detect_interval()

speakerDS, speakerEventDS, speakerFilt, micDS, micEventDS, micFilt =\
detect_events(
speakerDS, speakerEventDS, speakerFilt, micDS, micEventDS, micFilt = detect_events(
speaker_data=self.source_stim,
mic_data=self.source_resp,
interval=[self.detectStartBin, self.detectStopBin + 1],
Expand All @@ -350,7 +347,6 @@ def run_test(self):

self.draw_scene()


def run_detection(self):
self.set_detect_interval()
self.disable_all()
Expand Down Expand Up @@ -393,26 +389,23 @@ def out_close(self, val):
self.stimTimes = self.thread.stimTimes
self.respTimes = self.thread.respTimes

io = self.parent.model.io
nwb = self.parent.model.nwb

# Speaker stimuli times
ti_stim = TimeIntervals(name='TimeIntervals_speaker')
times = self.stimTimes.reshape((-1, 2)).astype('float')
for start, stop in times:
ti_stim.add_interval(start, stop)
self.parent.model.nwb.add_time_intervals(ti_stim)

# Microphone responses times
ti_resp = TimeIntervals(name='TimeIntervals_mic')
times = self.respTimes.reshape((-1, 2)).astype('float')
for start, stop in times:
ti_resp.add_interval(start, stop)
if self.respTimes is not None:
ti_resp = TimeIntervals(name='TimeIntervals_mic')
times = self.respTimes.reshape((-1, 2)).astype('float')
for start, stop in times:
ti_resp.add_interval(start, stop)
self.parent.model.nwb.add_time_intervals(ti_resp)

# Add both to file
nwb.add_time_intervals(ti_stim)
nwb.add_time_intervals(ti_resp)
# Write file
io.write(nwb)
self.parent.model.io.write(self.parent.model.nwb)

self.parent.model.refresh_file()
self.parent.model.SpeakerAndMicIntervalAdd()
Expand Down

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