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Event detection #3

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merged 8 commits into from Nov 7, 2019
Merged

Event detection #3

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f26987c
Adding smoothed signals and thresholds to event detection GUI after c…
emilyps14 Oct 27, 2019
51227e5
Improving the scaling and colors on the smoothed signals and thresholds
emilyps14 Oct 27, 2019
3d775ff
Allow the user to specify start and stop time for "whole signal" even…
emilyps14 Oct 27, 2019
268c1b5
Changing usage of the FS_colorLUT so that it will default to "unknown…
emilyps14 Oct 28, 2019
69782ce
Changing background color to white for unknown (when black it interfe…
emilyps14 Oct 28, 2019
0e83d76
In main application, plot the Speaker and Mic intervals if they exist
emilyps14 Oct 28, 2019
a929792
Updating the main window to show speaker and mic intervals after runn…
emilyps14 Oct 28, 2019
73bc318
Fix bug where ERPs with one row fill the height of the window
emilyps14 Oct 28, 2019
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18 changes: 9 additions & 9 deletions ecogvis/functions/FS_colorLUT.py
View file
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@@ -1,5 +1,5 @@
def get_lut():
cmap = {'Unknown': [ 0., 0., 0.],
cmap = {'Unknown': [ 255., 255., 255.],
'Left-Cerebral-Exterior': [70., 130., 180.],
'Left-Cerebral-White-Matter': [245., 245., 245.],
'Left-Cerebral-Cortex': [205., 62., 78.],
Expand Down Expand Up @@ -515,7 +515,7 @@ def get_lut():
'wm-rh-temporalpole': [185., 185., 185.],
'wm-rh-transversetemporal': [105., 105., 55.],
'wm-rh-insula': [254., 191., 31.],
'ctx-lh-Unknown': [0., 0., 0.],
'ctx-lh-Unknown': [255., 255., 255.],
'ctx-lh-Corpus_callosum': [50., 50., 50.],
'ctx-lh-G_and_S_Insula_ONLY_AVERAGE': [180., 20., 30.],
'ctx-lh-G_cingulate-Isthmus': [60., 25., 25.],
Expand Down Expand Up @@ -606,7 +606,7 @@ def get_lut():
'ctx-lh-S_temporal_inferior': [21., 180., 180.],
'ctx-lh-S_temporal_superior': [223., 220., 60.],
'ctx-lh-S_temporal_transverse': [221., 60., 60.],
'ctx-rh-Unknown': [0., 0., 0.],
'ctx-rh-Unknown': [255., 255., 255.],
'ctx-rh-Corpus_callosum': [50., 50., 50.],
'ctx-rh-G_and_S_Insula_ONLY_AVERAGE': [180., 20., 30.],
'ctx-rh-G_cingulate-Isthmus': [60., 25., 25.],
Expand Down Expand Up @@ -697,7 +697,7 @@ def get_lut():
'ctx-rh-S_pericallosal-caudal': [25., 150., 90.],
'ctx-rh-S_pericallosal-rostral': [25., 180., 90.],
'ctx-rh-S_pericallosal-posterior': [25., 210., 90.],
'wm-lh-Unknown': [0., 0., 0.],
'wm-lh-Unknown': [255., 255., 255.],
'wm-lh-Corpus_callosum': [50., 50., 50.],
'wm-lh-G_and_S_Insula_ONLY_AVERAGE': [180., 20., 30.],
'wm-lh-G_cingulate-Isthmus': [60., 25., 25.],
Expand Down Expand Up @@ -779,7 +779,7 @@ def get_lut():
'wm-lh-S_temporal_inferior': [21., 180., 180.],
'wm-lh-S_temporal_superior': [223., 220., 60.],
'wm-lh-S_temporal_transverse': [221., 60., 60.],
'wm-rh-Unknown': [0., 0., 0.],
'wm-rh-Unknown': [255., 255., 255.],
'wm-rh-Corpus_callosum': [50., 50., 50.],
'wm-rh-G_and_S_Insula_ONLY_AVERAGE': [180., 20., 30.],
'wm-rh-G_cingulate-Isthmus': [60., 25., 25.],
Expand Down Expand Up @@ -961,7 +961,7 @@ def get_lut():
'ctx-rh-posterior-parietal': [125., 120., 55.],
'ctx-rh-prim-sec-somatosensory': [225., 70., 105.],
'ctx-rh-occipital': [225., 70., 15.],
'ctx_lh_Unknown': [0., 0., 0.],
'ctx_lh_Unknown': [255., 255., 255.],
'ctx_lh_G_and_S_frontomargin': [23., 220., 60.],
'ctx_lh_G_and_S_occipital_inf': [23., 60., 180.],
'ctx_lh_G_and_S_paracentral': [63., 100., 60.],
Expand Down Expand Up @@ -1037,7 +1037,7 @@ def get_lut():
'ctx_lh_S_temporal_inf': [21., 180., 180.],
'ctx_lh_S_temporal_sup': [223., 220., 60.],
'ctx_lh_S_temporal_transverse': [221., 60., 60.],
'ctx_rh_Unknown': [0., 0., 0.],
'ctx_rh_Unknown': [255., 255., 255.],
'ctx_rh_G_and_S_frontomargin': [23., 220., 60.],
'ctx_rh_G_and_S_occipital_inf': [23., 60., 180.],
'ctx_rh_G_and_S_paracentral': [63., 100., 60.],
Expand Down Expand Up @@ -1113,7 +1113,7 @@ def get_lut():
'ctx_rh_S_temporal_inf': [21., 180., 180.],
'ctx_rh_S_temporal_sup': [223., 220., 60.],
'ctx_rh_S_temporal_transverse': [221., 60., 60.],
'wm_lh_Unknown': [0., 0., 0.],
'wm_lh_Unknown': [255., 255., 255.],
'wm_lh_G_and_S_frontomargin': [23., 220., 60.],
'wm_lh_G_and_S_occipital_inf': [23., 60., 180.],
'wm_lh_G_and_S_paracentral': [63., 100., 60.],
Expand Down Expand Up @@ -1189,7 +1189,7 @@ def get_lut():
'wm_lh_S_temporal_inf': [21., 180., 180.],
'wm_lh_S_temporal_sup': [223., 220., 60.],
'wm_lh_S_temporal_transverse': [221., 60., 60.],
'wm_rh_Unknown': [0., 0., 0.],
'wm_rh_Unknown': [255., 255., 255.],
'wm_rh_G_and_S_frontomargin': [23., 220., 60.],
'wm_rh_G_and_S_occipital_inf': [23., 60., 180.],
'wm_rh_G_and_S_paracentral': [63., 100., 60.],
Expand Down
128 changes: 93 additions & 35 deletions ecogvis/functions/subDialogs.py
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Open in desktop
Expand Up @@ -1042,7 +1042,7 @@ def draw_periodograms(self):
#Background
loc = 'ctx-lh-'+self.parent.model.nwb.electrodes['location'][ch]
vb = p.getViewBox()
color = tuple(cmap[loc])
color = tuple(cmap.get(loc, cmap['Unknown']))
vb.setBackgroundColor((*color,min(elem_alpha,70))) # append alpha to color tuple
#Main plots
if self.b1.isChecked() == True:
Expand Down Expand Up @@ -1169,7 +1169,7 @@ def draw_periodograms(self):
#Background
loc = 'ctx-lh-'+self.ancestor.model.nwb.electrodes['location'][self.ch]
vb = p.getViewBox()
color = tuple(cmap[loc])
color = tuple(cmap.get(loc, cmap['Unknown']))
vb.setBackgroundColor((*color,70)) # append alpha to color tuple
#Main plots
if self.b1.isChecked() == True:
Expand Down Expand Up @@ -1730,7 +1730,7 @@ def set_elec_group(self):
self.grid_order = np.where(self.electrodes.table['group_name'].data[:]==self.elec_group)[0]
self.nElecs = len(self.grid_order)
self.nCols = 16
self.nRows = int(self.nElecs/self.nCols)
self.nRows = max(int(self.nElecs/self.nCols),1)
self.set_grid()
self.draw_erp()

Expand Down Expand Up @@ -1949,7 +1949,7 @@ def draw_erp(self):
#Background
loc = 'ctx-lh-'+self.parent.model.nwb.electrodes['location'][ch]
vb = p.getViewBox()
color = tuple(cmap[loc])
color = tuple(cmap.get(loc, cmap['Unknown']))
vb.setBackgroundColor((*color,min(elem_alpha,70))) # append alpha to color tuple
#Main plots
mean = p.plot(x=X, y=Y_mean, pen=pg.mkPen((50,50,50,min(elem_alpha,255)), width=1.))
Expand Down Expand Up @@ -2132,7 +2132,7 @@ def draw_erp(self):
#Background color
loc = 'ctx-lh-'+self.parent.parent.parent.model.nwb.electrodes['location'][self.ch]
vb = p.getViewBox()
color = tuple(cmap[loc])
color = tuple(cmap.get(loc, cmap['Unknown']))
vb.setBackgroundColor((*color,70)) # append alpha to color tuple
vb.border = pg.mkPen(color = 'w')
#Main plots
Expand Down Expand Up @@ -2197,19 +2197,23 @@ def __init__(self, parent):
panel0.setLayout(grid0)

#Left panel - Detection ------------------------------------------------
labelDown = QLabel('Downsample:')
labelDown = QLabel('Downsample Factor:')
self.qline3 = QLineEdit('800')
labelDown.setToolTip('Downsample rate of raw signal.\n'
'Typical values: 500~900 Hz')
labelWidth = QLabel('Width:')
labelWidth = QLabel('Kernel Width:')
self.qline4 = QLineEdit('.4')
labelWidth.setToolTip('This will affect the width of \n'
'the smoothing filter.\n'
'the smoothing filter (seconds).\n'
'Typical values: .1 ~ 1')
labelThresh = QLabel('Threshold:')
labelSpeakerThresh = QLabel('Speaker Threshold:')
self.qline5 = QLineEdit('.05')
labelThresh.setToolTip('This will affect the sensitivity to variation.\n'
labelSpeakerThresh.setToolTip('Threshold on the smoothed signal (standard deviations from the mean).\n'
'Typical values: .02 ~ .1')
labelMicThresh = QLabel('Mic Threshold:')
self.qline6 = QLineEdit('.1')
labelMicThresh.setToolTip('Threshold on the smoothed signal (standard deviations from the mean).\n'
'Typical values: .05 ~ .5')
self.push1_0 = QPushButton('Run Test')
self.push1_0.clicked.connect(self.run_test)

Expand All @@ -2218,18 +2222,30 @@ def __init__(self, parent):
grid1.addWidget(self.qline3, 0, 4, 1, 2)
grid1.addWidget(labelWidth, 1, 0, 1, 4)
grid1.addWidget(self.qline4, 1, 4, 1, 2)
grid1.addWidget(labelThresh, 2, 0, 1, 4)
grid1.addWidget(labelSpeakerThresh, 2, 0, 1, 4)
grid1.addWidget(self.qline5, 2, 4, 1, 2)
grid1.addWidget(self.push1_0, 3, 0, 1, 6)
grid1.addWidget(labelMicThresh, 3, 0, 1, 4)
grid1.addWidget(self.qline6, 3, 4, 1, 2)
grid1.addWidget(self.push1_0, 4, 0, 1, 6)
grid1.setAlignment(QtCore.Qt.AlignTop)
panel1 = QGroupBox('Detection Parameters')
panel1.setFixedWidth(200)
panel1.setLayout(grid1)

labelDetectStart = QLabel('Start [sec]:')
self.qline7 = QLineEdit('0')
self.qline7.returnPressed.connect(self.reset_draw)
labelDetectStop = QLabel('Stop [sec]:')
self.qline8 = QLineEdit('end')
self.qline8.returnPressed.connect(self.reset_draw)
self.push2_0 = QPushButton('Run Detection')
self.push2_0.clicked.connect(self.run_detection)
grid2 = QGridLayout()
grid2.addWidget(self.push2_0)
grid2.addWidget(labelDetectStart, 0, 0, 1, 4)
grid2.addWidget(self.qline7, 0, 4, 1, 2)
grid2.addWidget(labelDetectStop, 1, 0, 1, 4)
grid2.addWidget(self.qline8, 1, 4, 1, 2)
grid2.addWidget(self.push2_0, 2, 0, 1, 6)
panel2 = QGroupBox('Run for whole signal')
panel2.setFixedWidth(200)
panel2.setLayout(grid2)
Expand Down Expand Up @@ -2312,9 +2328,26 @@ def set_interval(self):
self.plotBins = np.clip(self.plotBins, 0, self.nTotalBins-1).astype('int')
self.x = self.plotBins/self.fs

def set_detect_interval(self):
"""Sets new detect interval"""
# Control for invalid values and ranges
if self.qline8.text()=='end':
self.qline8.setText(str(np.round(self.maxTime,1)))
self.detectStartTime = np.clip(float(self.qline7.text()), 0, self.maxTime-1.1)
self.detectStopTime = np.clip(float(self.qline8.text()), 1.1, self.maxTime)
if (self.detectStopTime-self.detectStartTime)<1:
self.detectStopTime = self.detectStartTime + 1
self.qline7.setText(str(np.round(self.detectStartTime,1)))
self.qline8.setText(str(np.round(self.detectStopTime,1)))
#Calculate correspondent bins
self.detectStartBin = int(self.detectStartTime*self.fs)
self.detectStopBin = int(self.detectStopTime*self.fs)


def draw_scene(self):
"""Draws signal and detection points."""
self.set_interval()
self.set_detect_interval()
self.win.clear()
#self.win.addLegend()
#Plot stimuli
Expand All @@ -2335,29 +2368,39 @@ def draw_scene(self):
self.win.getAxis('bottom').setPen(pg.mkPen(color=(50,50,50)))

def run_test(self):
speakerDS, speakerEventDS, micDS, micEventDS = detect_events(
speaker_data=self.source_stim,
mic_data=self.source_resp,
interval=[self.plotBins[0],self.plotBins[-1]+1],
dfact=self.fs/float(self.qline3.text()),
smooth_width=float(self.qline4.text()),
threshold=float(self.qline5.text()))
speakerDS, speakerEventDS, speakerFilt, speakerThresh, \
micDS, micEventDS, micFilt, micThresh \
= detect_events(speaker_data=self.source_stim,
mic_data=self.source_resp,
interval=[self.plotBins[0],self.plotBins[-1]+1],
dfact=self.fs/float(self.qline3.text()),
smooth_width=float(self.qline4.text()),
speaker_threshold=float(self.qline5.text()),
mic_threshold=float(self.qline6.text()))
self.stimTimes = speakerEventDS + self.startTime
self.respTimes = micEventDS + self.startTime
#self.draw_scene()
self.xx = self.startTime + np.arange(len(speakerDS))/float(self.qline3.text())
self.win.clear()
#self.win.addLegend()
#Plot speaker
y0 = speakerDS
y0 /= np.max(np.abs(y0))
self.win.plot(self.xx, y0+2, pen=pg.mkPen((0,0,200), width=1.), name='Speaker')
y0 = np.stack([speakerDS, speakerFilt, np.ones(speakerDS.shape)*speakerThresh],axis=1)
y0[:,0] /= np.max(np.abs(y0[:,0]))
y0[:,1:] /= np.max(np.abs(y0[:,1]))
y0_names = ['Speaker','SpeakerFilt','SpeakerThresh']
y0_kargs = [{'color':(0,0,200),'width':1.},{'color':(0,200,200),'width':2.},{'color':(0,200,200),'width':1.,'style':QtCore.Qt.DashLine}]
for name,kargs,column in zip(y0_names,y0_kargs,y0.T):
self.win.plot(self.xx, column+2, pen=pg.mkPen(**kargs), name=name)
for st in self.stimTimes:
self.win.plot([st, st], [0, 3], pen=pg.mkPen((0,0,200), width=2.))
#Plot responses
y1 = micDS
y1 /= np.max(np.abs(y1))
self.win.plot(self.xx, y1+1, pen=pg.mkPen((200,0,0), width=1.), name='Mic')
y1 = np.stack([micDS, micFilt,np.ones(micDS.shape)*micThresh],axis=1)
y1[:,0] /= np.max(np.abs(y1[:,0]))
y1[:,1:] /= np.max(np.abs(y1[:,1]))
y1_names = ['Mic','MicFilt','MicThresh']
y1_kargs = [{'color':(200,0,0),'width':1.},{'color':(0,0,0),'width':2.},{'color':(0,0,0),'width':1.,'style':QtCore.Qt.DashLine}]
for name,kargs,column in zip(y1_names,y1_kargs,y1.T):
self.win.plot(self.xx, column+1, pen=pg.mkPen(**kargs), name=name)
for rt in self.respTimes:
self.win.plot([rt, rt], [0, 3], pen=pg.mkPen((200,0,0), width=2.))
#Axes parameters
Expand All @@ -2370,13 +2413,17 @@ def run_test(self):
self.win.getAxis('bottom').setPen(pg.mkPen(color=(50,50,50)))

def run_detection(self):
self.set_detect_interval()
self.disable_all()
self.plotTitle.setText('Running event detection. Please wait...')
self.plotTitle.setText(f'Running event detection {self.detectStartTime}-{self.detectStopTime}s. Please wait...')
self.thread = EventDetectionFunction(speaker_data=self.source_stim,
mic_data=self.source_resp,
interval=[self.detectStartBin,self.detectStopBin+1],
time_offset=self.detectStartTime,
dfact=self.fs/float(self.qline3.text()),
smooth_width=float(self.qline4.text()),
threshold=float(self.qline5.text()))
speaker_threshold=float(self.qline5.text()),
mic_threshold=float(self.qline6.text()))
self.thread.finished.connect(lambda: self.out_close(1))
self.thread.start()

Expand All @@ -2390,6 +2437,9 @@ def disable_all(self):
self.qline3.setEnabled(False)
self.qline4.setEnabled(False)
self.qline5.setEnabled(False)
self.qline6.setEnabled(False)
self.qline7.setEnabled(False)
self.qline8.setEnabled(False)
self.push1_0.setEnabled(False)
self.push2_0.setEnabled(False)

Expand All @@ -2416,27 +2466,35 @@ def out_close(self, val):
nwb.add_time_intervals(ti_resp)
#Write file
io.write(nwb)
self.parent.model.refresh_file()
self.parent.model.SpeakerAndMicIntervalAdd()
self.parent.model.refreshScreen()
self.accept()


# Runs 'detect_events' function, useful to wait for thread ---------------------
class EventDetectionFunction(QtCore.QThread):
def __init__(self, speaker_data, mic_data, dfact, smooth_width, threshold):
def __init__(self, speaker_data, mic_data, interval, time_offset, dfact, smooth_width,
speaker_threshold, mic_threshold):
super().__init__()
self.source_stim = speaker_data
self.source_resp = mic_data
self.interval = interval
self.time_offset = time_offset
self.dfact = dfact
self.smooth_width = smooth_width
self.threshold = threshold
self.stim_threshold = speaker_threshold
self.resp_threshold = mic_threshold

def run(self):
speakerDS, speakerEventDS, micDS, micEventDS = detect_events(
speakerDS, speakerEventDS, _, _, micDS, micEventDS, _, _ = detect_events(
speaker_data=self.source_stim,
mic_data=self.source_resp,
interval=None,
interval=self.interval,
dfact=self.dfact,
smooth_width=self.smooth_width,
threshold=self.threshold,
speaker_threshold=self.stim_threshold,
mic_threshold=self.resp_threshold,
direction='both')
self.stimTimes = speakerEventDS
self.respTimes = micEventDS
self.stimTimes = speakerEventDS + self.time_offset
self.respTimes = micEventDS + self.time_offset
20 changes: 20 additions & 0 deletions ecogvis/functions/subFunctions.py
View file
Open in desktop
Expand Up @@ -117,6 +117,9 @@ def __init__(self, par):
c.setBrush(QtGui.QColor(255, 0, 0, 120))
self.parent.win1.addItem(c)

# Add Speaker and Mic Intervals if they exist
self.SpeakerAndMicIntervalAdd()

# Load stimuli signals (audio)
self.load_stimuli()

Expand Down Expand Up @@ -698,6 +701,23 @@ def IntervalLoad(self, fname):
self.refreshScreen()


def SpeakerAndMicIntervalAdd(self):
if self.nwb.intervals is not None:
keys = ['TimeIntervals_speaker','TimeIntervals_mic']
colors = ['blue','green']
for name,color in zip(keys,colors):
if name in self.nwb.intervals:
ti = self.nwb.intervals[name]
nI = len(ti)
for ii in np.arange(nI):
interval = [ti['start_time'][ii], ti['stop_time'][ii]]
int_type = name
color = color
session = ''
self.IntervalAdd(interval, int_type, color, session)



# Channels functions -------------------------------------------------------
def BadChannelAdd(self, ch_list):
"""
Expand Down