def event_cut(self):
# Get cutting parameters
try:
baseline = float(self.eventBaseline.text()) / self.dt
duration = float(self.eventDuration.text()) / self.dt
except NameError:
aux.error_box('Invalid cutting value')
# Cut out
events, allAttrs = [], []
for onset in self.xOnsets:
eStart = onset - baseline
eEnd = onset + duration
eData = self.trace[eStart:eEnd]
events.append(eData)
attrs = {}
attrs['dt'] = self.dt
attrs['onset'] = onset
allAttrs.append(attrs)
# Store event waveforms in h5 data tree
results = []
#attrs = {}
#attrs['dt'] = self.dt
for e in np.arange(0, len(events)):
#attrs['onset'] = self.xOnsets[e]
results.append(['event' + str(e), events[e], allAttrs[e]])
aux.save_results(self.browser, 'Events', results)
def event_cut(self):
# Get cutting parameters
try:
baseline = float(self.eventBaseline.text())/self.dt
duration = float(self.eventDuration.text())/self.dt
except NameError:
aux.error_box('Invalid cutting value')
# Cut out
events, allAttrs = [], []
for onset in self.xOnsets:
eStart = onset-baseline
eEnd = onset+duration
eData = self.trace[eStart:eEnd]
events.append(eData)
attrs = {}
attrs['dt'] = self.dt
attrs['onset'] = onset
allAttrs.append(attrs)
# Store event waveforms in h5 data tree
results = []
#attrs = {}
#attrs['dt'] = self.dt
for e in np.arange(0, len(events)):
#attrs['onset'] = self.xOnsets[e]
results.append(['event'+str(e), events[e], allAttrs[e]])
aux.save_results(self.browser, 'Events', results)
def event_cut(self):
# Get trace and event onsets using stored dataIndex
itrace = self.eventItemsIndex[0]
trace = self.browser.ui.workingDataTree.dataItems[itrace]
ionsets = self.eventItemsIndex[1]
onsets = self.browser.ui.workingDataTree.dataItems[ionsets]
dt = float(trace.attrs['dt'])
# Get cutting parameters
baseline = float(self.eventBaseline.text())/dt
duration = float(self.eventDuration.text())/dt
# Cut out
events = []
for onset in onsets.data:
eStart = onset-baseline
eEnd = onset+duration
eData = trace.data[eStart:eEnd]
events.append(eData)
# Store event waveforms in h5 data tree
results = []
attrs = {}
attrs['dt'] = dt
for e in np.arange(0, len(events)):
results.append(['event'+str(e), events[e], attrs])
aux.save_results(self.browser, 'Events', results)
def func(self, browser):
""" Measure selected properties or statistics in the region defined
by the data cursors.
Options:
1) create new entries in Working Data tree with the results
"""
############################################
# ANALYSIS FUNCTION
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
data = aux.get_data(browser)
c1, c2 = aux.get_cursors(plotWidget)
dataIndex = plotWidget.plotDataIndex
saveData = False
# Get dt list
dtList = aux.get_attr(plotWidget.plotDataItems, 'dt')
# Go through data and check selected values to measure
# Can probably do this in a more efficient way
results = []
for option in self.toolOptions:
if option.isChecked():
if option.text()=='Store result':
saveData = True
if option.text()=='Minimum':
dataMin = []
for t in range(len(data)):
dt = dtList[t]
y = np.min(data[t][c1/dt:c2/dt])
x = np.argmin(data[t][c1/dt:c2/dt])
dataMin.append(y)
aux.plot_point(plotWidget, c1/dt, x, y, dt)
results.append(['Minimum', dataMin])
if option.text()=='Maximum':
dataMax = []
for t in range(len(data)):
dt = dtList[t]
y = np.max(data[t][c1/dt:c2/dt])
x = np.argmax(data[t][c1/dt:c2/dt])
dataMax.append(y)
aux.plot_point(plotWidget, c1/dt, x, y, dt)
results.append(['Maximum', dataMax])
if option.text()=='Mean':
dataMean = []
for t in range(len(data)):
dt = dtList[t]
y = np.mean(data[t][c1/dt:c2/dt])
dataMean.append(y)
plotWidget.plot([c1,c2], [y,y], pen=pg.mkPen('#CF1C04', width=1))
results.append(['Mean', dataMean])
# Store results
if saveData: aux.save_results(browser, 'Measurements', results)
def func(self, browser):
""" Filter traces
Options:
1) Filter type (currently Bessel only)
2) Filter parameters
Note: filter frequencies are in Hz, make sure dt is in seconds
"""
############################################
# ANALYSIS FUNCTION
# Get options
btype = str(self.comboPass.currentText())
if 'Low' in btype:
btype = 'low'
elif 'High' in btype:
btype = 'high'
try:
cutoff = float(self.filterCutoff.text())
order = float(self.filterOrder.text())
except ValueError:
aux.error_box('Invalid Cut off or Order value')
return
bidir = self.filterDirection.isChecked()
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Filter data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['filter_type'] = btype
attrs['filter_cutoff'] = cutoff
attrs['filter_order'] = order
# Filter
traceFilter = acq4filter.besselFilter(item.data, cutoff, order, float(item.attrs['dt'])/1000, btype, bidir)
results.append([item.text(0), traceFilter, attrs])
# Store filtered traces
filterItem = aux.make_h5item('filter', traceFilter, item.attrs)
itemsToPlot.append(filterItem)
# Plot results
pgplot.plot_multipleData(browser, plotWidget, itemsToPlot, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_filter', results)
def func(self, browser):
""" Smooth traces
Options:
1) Window type
2) Window length
"""
############################################
# ANALYSIS FUNCTION
# Get options
window = str(self.comboBox.currentText())
try:
window_len = float(self.smoothLength.text())
except ValueError:
aux.error_box('Invalid Window Length')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Smooth data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['smooth_window_type'] = window
attrs['smooth_window_length'] = window_len
# Smooth
traceSmooth = smooth.smooth(item.data,
window_len=window_len,
window=window)
results.append([item.text(0), traceSmooth, attrs])
# Store smoothed item
smoothItem = aux.make_h5item('smooth', traceSmooth, item.attrs)
itemsToPlot.append(smoothItem)
# Plot results
pgplot.plot_multipleData(browser,
plotWidget,
itemsToPlot,
clear=False,
color='#F2EF44')
# Store results
aux.save_results(browser, parentText + '_smooth', results)
def func(self, browser):
""" Remove a specific frequency from the data
Options:
1) Frequency
2) Number of harmonics
3) Number of FFT data samples to blank centered on the Frequency
4) Scale factor for how much the frequency is dampened (0<x<1)
Note: frequencies are in Hz, make sure dt is in seconds
"""
############################################
# ANALYSIS FUNCTION
# Get options
frequency = float(self.freqRemoveFrequency.text())
harmonics = int(self.freqRemoveHarmonics.text())
samples = int(self.freqRemoveSamples.text())
mag = float(self.freqRemoveMag.text())
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Remove frequency
results = []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['frequency_removed'] = frequency
# Remove
traceFilter = acq4filter.removePeriodic(
item.data, frequency,
float(item.attrs['dt']) / 1000, harmonics, samples, mag)
results.append([item.text(0), traceFilter, attrs])
# Store and plot filtered trace
filterItem = aux.make_h5item('filter', traceFilter, item.attrs)
pgplot.browse_singleData(browser,
plotWidget,
filterItem,
clear=False,
color='#F2EF44')
# Store results
aux.save_results(browser, parentText + '_filter', results)
def func(self, browser):
""" Average trials for protocols with more than one sweep
(e.g.: current or voltage steps)
Options:
1) Number of trials contained in the selected traces
"""
############################################
# ANALYSIS FUNCTION
# Get options
try:
numberOfTrials = int(self.trialsNumber.text())
except ValueError:
aux.error_box('Please input a valid number of trials')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Get data and attributes
data = aux.get_data(self.browser)
item = plotWidget.plotDataItems[0]
# Reshape data and average
try:
data.shape = (numberOfTrials, data.shape[0]/numberOfTrials, data.shape[1])
avg = data.mean(axis=0)
# Make h5 items
results, itemsToPlot = [], []
for sweep in avg:
#sweepItem = aux.make_h5item('sweep', sweep, item.attrs)
results.append(['sweep', sweep, item.attrs])
# Store average sweep
sweepItem = aux.make_h5item('sweep', sweep, item.attrs)
itemsToPlot.append(sweepItem)
# Plot results
pgplot.plot_multipleData(browser, plotWidget, itemsToPlot, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_trialsAvg', results)
except ValueError:
aux.error_box('The number of sweeps and trials do not match', sys.exc_info())
def func(self, browser):
""" Downsample data by taking one point every N points
Options:
1) Number of points
"""
############################################
# ANALYSIS FUNCTION
# Get options
try:
nPoints = int(self.points.text())
except ValueError:
aux.error_box('Invalid number of points')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Smooth data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = dict(item.attrs)
attrs['dt'] = attrs['dt'] * nPoints
# Downsample
traceDsampled = item.data[0::nPoints]
results.append([item.text(0), traceDsampled, attrs])
# Store smoothed item
dSampledItem = aux.make_h5item('smooth', traceDsampled, attrs)
itemsToPlot.append(dSampledItem)
# Plot results
pgplot.plot_multipleData(browser,
plotWidget,
itemsToPlot,
clear=False,
color='#F2EF44')
# Store results
aux.save_results(browser, parentText + '_dSample', results)
def func(self, browser):
""" Smooth traces
Options:
1) Window type
2) Window length
"""
############################################
# ANALYSIS FUNCTION
# Get options
window = str(self.comboBox.currentText())
try:
window_len = float(self.smoothLength.text())
except ValueError:
aux.error_box('Invalid Window Length')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Smooth data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['smooth_window_type'] = window
attrs['smooth_window_length'] = window_len
# Smooth
traceSmooth = smooth.smooth(item.data, window_len=window_len, window=window)
results.append([item.text(0), traceSmooth, attrs])
# Store smoothed item
smoothItem = aux.make_h5item('smooth', traceSmooth, item.attrs)
itemsToPlot.append(smoothItem)
# Plot results
pgplot.plot_multipleData(browser, plotWidget, itemsToPlot, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_smooth', results)
def func(self, browser):
""" Remove a specific frequency from the data
Options:
1) Frequency
2) Number of harmonics
3) Number of FFT data samples to blank centered on the Frequency
4) Scale factor for how much the frequency is dampened (0<x<1)
Note: frequencies are in Hz, make sure dt is in seconds
"""
############################################
# ANALYSIS FUNCTION
# Get options
frequency = float(self.freqRemoveFrequency.text())
harmonics = int(self.freqRemoveHarmonics.text())
samples = int(self.freqRemoveSamples.text())
mag = float(self.freqRemoveMag.text())
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Remove frequency
results = []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['frequency_removed'] = frequency
# Remove
traceFilter = acq4filter.removePeriodic(item.data, frequency,
float(item.attrs['dt'])/1000, harmonics, samples, mag)
results.append([item.text(0), traceFilter, attrs])
# Store and plot filtered trace
filterItem = aux.make_h5item('filter', traceFilter, item.attrs)
pgplot.browse_singleData(browser, plotWidget, filterItem, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_filter', results)
def func(self, browser):
""" Downsample data by taking one point every N points
Options:
1) Number of points
"""
############################################
# ANALYSIS FUNCTION
# Get options
try:
nPoints = int(self.points.text())
except ValueError:
aux.error_box('Invalid number of points')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Smooth data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = dict(item.attrs)
attrs['dt'] = attrs['dt']*nPoints
# Downsample
traceDsampled = item.data[0::nPoints]
results.append([item.text(0), traceDsampled, attrs])
# Store smoothed item
dSampledItem = aux.make_h5item('smooth', traceDsampled, attrs)
itemsToPlot.append(dSampledItem)
# Plot results
pgplot.plot_multipleData(browser, plotWidget, itemsToPlot, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_dSample', results)
def func(self, browser):
""" Smooth traces
Options:
1) Window type
2) Window length
"""
############################################
# ANALYSIS FUNCTION
# Get options
window = str(self.comboBox.currentText())
window_len = float(self.smoothLength.text())
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Smooth data
results = []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['smooth_window_type'] = window
attrs['smooth_window_length'] = window_len
# Smooth
traceSmooth = smooth.smooth(item.data, window_len=window_len, window=window)
results.append([item.text(0), traceSmooth, attrs])
# Plot smoothed trace
#x = np.arange(0, len(traceSmooth)*item.attrs['dt'], item.attrs['dt'])
#plotWidget.plot(x, traceSmooth, pen=pg.mkPen('#F2EF44', width=1))
smoothItem = aux.make_h5item('smooth', traceSmooth, item.attrs)
pgplot.browse_singleData(browser, plotWidget, smoothItem, clear=False, color='#F2EF44')
# Store results
aux.save_results(browser, parentText+'_smooth', results)
def func(self, browser):
""" Calculate average trace from currently plotted traces.
Options:
1) create new entry in Working Data tree with the result
2) plot average with orginal traces
"""
############################################
# ANALYSIS FUNCTION
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Clear plot and get data
plotWidget.clear()
data = aux.get_data(browser)
# Get dt and
dt = aux.get_attr(plotWidget.plotDataItems, 'dt')[0]
# Calculate average
avgData = np.mean(data,0)
# Check selected options
for option in self.toolOptions:
if option.isChecked():
if option.text()=='Store result':
results = []
# Get attributes from plotted items
item = plotWidget.plotDataItems[0]
attrs = item.attrs
# Store data
results.append(['avg_trace', avgData, attrs])
aux.save_results(browser, item.parent().text(0)+'_average', results)
if option.text()=='Show traces':
pgplot.replot(browser, plotWidget)
# Plot average
item = aux.make_h5item('avg', avgData, plotWidget.plotDataItems[0].attrs)
pgplot.browse_singleData(browser, plotWidget, item, clear=False, color='r')
if browser.ui.actionShowCursors.isChecked(): pgplot.replot_cursors(browser, plotWidget)
def event_cut(self, profile=False):
# Read options
baseline = float(self.eventBaseline.text())
duration = float(self.eventDuration.text())
# Get plotted tracking data
trackData = self.plotWidget.plotDataItems[0].data
# Get selected trigger data
item = self.browser.ui.workingDataTree.currentItem()
triggers = item.data
# Deal with dt
dt = self.plotWidget.plotDataItems[0].attrs['dt']
item.attrs['dt'] = dt
# Extract events
events, stimProfiles = [], []
for t in self.tevents:
event = trackData[t-int(baseline/dt):t+int(duration/dt)]
events.append(event)
if profile:
eventProfile = self.triggerProfileData[t-int(baseline/dt):t+int(duration/dt)]
stimProfiles.append(eventProfile)
# Store data
results = []
attrs = {}
attrs['dt'] = dt
attrs['t0'] = baseline # in sampling points
for e in np.arange(0, len(events)):
attrs['trigger_time'] = self.tevents[e] # in sampling points
results.append(['event'+str(e), events[e], attrs])
aux.save_results(self.browser, 'Events', results)
if profile:
results = []
for e in np.arange(0, len(stimProfiles)):
attrs['trigger_time'] = self.tevents[e] # in sampling points
results.append(['stim'+str(e), stimProfiles[e], attrs])
aux.save_results(self.browser, 'Stimulation Profiles', results)
def func(self, browser):
""" Analyse tracking data for user defined zones in
the arena. Currently the two zones are defined by
a divider on the X or Y coordinates.
Properties measured:
1 - time spent in each zone normalized to total time
2 - number of zone transitions
Options:
1) Position of the divider between the two zones
"""
############################################
# ANALYSIS FUNCTION
# Read options
zoneDivider = float(self.plotWidget.zoneDividerCursorPos)
# Get data and check cursors
traces = self.plotWidget.plotDataItems
dt = traces[0].attrs['dt']
data, c1 = aux.get_dataRange(self.plotWidget, traces[0])
# Get time in each zone
zoneTime = []
totalTime = float(len(data))
zone1 = np.sum(data < zoneDivider)
zone2 = totalTime - zone1
zoneTime.append(zone1 / totalTime)
zoneTime.append(zone2 / totalTime)
# Get number of zone transitions
transitions = np.sum(np.diff(data < zoneDivider))
# Store data
results = []
results.append(['Time', zoneTime])
results.append(['Transitions', [transitions]])
aux.save_results(self.browser, 'Zone_analysis', results)
def func(self, browser):
""" Temporary event detection function using amplitude
threshold only. Noise safety is for when coming down from
peak, go down an extra amount from threshold before starting
to search for the next event.
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
try:
noiseSafety = float(self.eventNoiseSafety.text())
smoothFactor = float(self.eventSmooth.text())
direction = str(self.eventDirection.currentText())
minDuration = float(self.eventMinDuration.text())
detectionTrace = str(self.detectionTrace.currentText())
minInterval = float(self.eventMinInterval.text())
except NameError:
aux.error_box('Invalid detection value')
bslWindow = 1.0
slowestRise = 0.5
#minEventInterval = 5000.0
# Ensure that noise safety has the same sign as the threshold
noiseSafety = np.sign(threshold) * abs(noiseSafety)
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
# Get dt list and attrs for use in concatenated data
dtList = aux.get_attr(self.browser.ui.dataPlotsWidget.plotDataItems, 'dt')
dt = dtList[0]
self.dt = dt
item = self.browser.ui.dataPlotsWidget.plotDataItems[0]
attrs = item.attrs
# Get data currently plotted and concatenate in a single sweep
data = []
for item in plotWidget.plotDataItems:
trace, c1 = aux.get_dataRange(plotWidget, item)
data.append(trace)
data = np.array(data).ravel()
# Get derivative trace and filter
dtrace = None
if detectionTrace=='derivative':
print threshold
dtrace = np.diff(data)
dtrace = acq4filter.besselFilter(dtrace, 2000, 1, dt/1000, 'low', True)
# Smooth
self.trace = data
if smoothFactor > 1:
data = smooth.smooth(data, window_len=smoothFactor, window='hanning')
# Comparison functions
if direction=='negative':
comp = lambda a, b: a < b
elif direction=='positive':
comp = lambda a, b: a > b
# Correct times for dt
minEventInterval = minInterval/dt
minDuration = minDuration/dt
bslWindow = bslWindow/dt
slowestRise = slowestRise/dt
# Run detection
eventCounter,i = 0,0 #+bslWindow/dt+slowestRise/dt
iLastDetection = 0
self.xOnsets, self.yOnsets = [], []
bsl = 0
if dtrace is not None:
detectionData = dtrace
else:
detectionData = data
while i<len(detectionData):
# Sliding baseline
#bsl = np.mean(data[i-bslWindow-slowestRise:i])
if comp(detectionData[i]-bsl,threshold):
print i, i-iLastDetection
if i-iLastDetection>minEventInterval: # Min inter-event interval
self.xOnsets.append(i)
self.yOnsets.append(data[i])
eventCounter+=1
iLastDetection = i
while i<len(detectionData) and comp(detectionData[i]-bsl,(threshold-noiseSafety)):
i+=1 # skip values if index in bounds AND until the value is below/above threshold again
if i-iLastDetection < minDuration: # Event is too brief
self.xOnsets.pop()
self.yOnsets.pop()
eventCounter-=1
else:
i+=1 # for min event interval
else:
i+=1
frequency = eventCounter/(len(data)*dt)*1000 # in Hz
print eventCounter, 'events detected at', frequency, 'Hz'
# Store event onsets and peaks in h5 data tree
results = []
results.append(['trace', np.array(self.trace), attrs])
results.append(['xOnsets', np.array(self.xOnsets)])
results.append(['yOnsets', np.array(self.yOnsets)])
results.append(['number', np.array([eventCounter])])
results.append(['frequency', np.array([frequency])])
aux.save_results(browser, 'Event_Detection', results)
# Plot results
self.show_events(data, np.array(self.xOnsets), np.array(self.yOnsets), dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
def func(self, browser):
""" Temporary event detection function using amplitude
threshold only. Noise safety is for when coming down from
peak, go down an extra amount from threshold before starting
to search for the next event.
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
noiseSafety = float(self.eventNoiseSafety.text())
smoothFactor = float(self.eventSmooth.text())
direction = str(self.eventDirection.currentText())
c1, c2 = aux.get_cursors(self.browser.ui.dataPlotsWidget)
# Ensure that noise safety has the same sign as the threshold
noiseSafety = np.sign(threshold) * abs(noiseSafety)
# Get dt list and attrs for use in concatenated data
dtList = aux.get_attr(self.browser.ui.dataPlotsWidget.plotDataItems, 'dt')
dt = dtList[0]
item = self.browser.ui.dataPlotsWidget.plotDataItems[0]
attrs = item.attrs
# Get data currently plotted within the cursors and concatenate in a single sweep
data = aux.get_data(self.browser)
if browser.ui.dataPlotsWidget.cursor1Pos: data = data[:,c1/dt:c2/dt]
data = data.ravel()
# Smooth
original_data = data
if smoothFactor > 1:
data = smooth.smooth(data, window_len=smoothFactor, window='hanning')
# Run detection
if direction=='negative':
comp = lambda a, b: a < b
elif direction=='positive':
comp = lambda a, b: a > b
eventCounter,i = 0,0
xOnsets, yOnsets = [], []
while i<len(data):
if comp(data[i],threshold):
xOnsets.append(i)
yOnsets.append(data[i])
eventCounter +=1
while i<len(data) and comp(data[i],(threshold-noiseSafety)):
i+=1 # skip values if index in bounds AND until the value is below/above threshold again
else:
i+=1
frequency = eventCounter/(len(data)*dt)*1000 # in Hz
print eventCounter, 'events detected at', frequency, 'Hz'
# Store event onsets and peaks in h5 data tree
results = []
results.append(['trace', np.array(original_data), attrs])
results.append(['onsets', np.array(xOnsets)])
results.append(['peaks', np.array(yOnsets)])
results.append(['number', np.array([eventCounter])])
results.append(['frequency', np.array([frequency])])
listIndexes = aux.save_results(browser, 'Event_Detection', results)
# Store list indexes temporarily in stack widget list for further event analysis
self.eventItemsIndex = listIndexes
# Plot results
self.show_events(data, np.array(xOnsets), np.array(yOnsets), dt)
def func(self, browser):
""" Temporary event detection function using amplitude
threshold only. Noise safety is for when coming down from
peak, go down an extra amount from threshold before starting
to search for the next event.
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
try:
noiseSafety = float(self.eventNoiseSafety.text())
smoothFactor = float(self.eventSmooth.text())
direction = str(self.eventDirection.currentText())
minDuration = float(self.eventMinDuration.text())
detectionTrace = str(self.detectionTrace.currentText())
minInterval = float(self.eventMinInterval.text())
except NameError:
aux.error_box('Invalid detection value')
bslWindow = 1.0
slowestRise = 0.5
#minEventInterval = 5000.0
# Ensure that noise safety has the same sign as the threshold
noiseSafety = np.sign(threshold) * abs(noiseSafety)
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
# Get dt list and attrs for use in concatenated data
dtList = aux.get_attr(self.browser.ui.dataPlotsWidget.plotDataItems,
'dt')
dt = dtList[0]
self.dt = dt
item = self.browser.ui.dataPlotsWidget.plotDataItems[0]
attrs = item.attrs
# Get data currently plotted and concatenate in a single sweep
data = []
for item in plotWidget.plotDataItems:
trace, c1 = aux.get_dataRange(plotWidget, item)
data.append(trace)
data = np.array(data).ravel()
# Get derivative trace and filter
dtrace = None
if detectionTrace == 'derivative':
print threshold
dtrace = np.diff(data)
dtrace = acq4filter.besselFilter(dtrace, 2000, 1, dt / 1000, 'low',
True)
# Smooth
self.trace = data
if smoothFactor > 1:
data = smooth.smooth(data,
window_len=smoothFactor,
window='hanning')
# Comparison functions
if direction == 'negative':
comp = lambda a, b: a < b
elif direction == 'positive':
comp = lambda a, b: a > b
# Correct times for dt
minEventInterval = minInterval / dt
minDuration = minDuration / dt
bslWindow = bslWindow / dt
slowestRise = slowestRise / dt
# Run detection
eventCounter, i = 0, 0 #+bslWindow/dt+slowestRise/dt
iLastDetection = 0
self.xOnsets, self.yOnsets = [], []
bsl = 0
if dtrace is not None:
detectionData = dtrace
else:
detectionData = data
while i < len(detectionData):
# Sliding baseline
#bsl = np.mean(data[i-bslWindow-slowestRise:i])
if comp(detectionData[i] - bsl, threshold):
print i, i - iLastDetection
if i - iLastDetection > minEventInterval: # Min inter-event interval
self.xOnsets.append(i)
self.yOnsets.append(data[i])
eventCounter += 1
iLastDetection = i
while i < len(detectionData) and comp(
detectionData[i] - bsl, (threshold - noiseSafety)):
i += 1 # skip values if index in bounds AND until the value is below/above threshold again
if i - iLastDetection < minDuration: # Event is too brief
self.xOnsets.pop()
self.yOnsets.pop()
eventCounter -= 1
else:
i += 1 # for min event interval
else:
i += 1
frequency = eventCounter / (len(data) * dt) * 1000 # in Hz
print eventCounter, 'events detected at', frequency, 'Hz'
# Store event onsets and peaks in h5 data tree
results = []
results.append(['trace', np.array(self.trace), attrs])
results.append(['xOnsets', np.array(self.xOnsets)])
results.append(['yOnsets', np.array(self.yOnsets)])
results.append(['number', np.array([eventCounter])])
results.append(['frequency', np.array([frequency])])
aux.save_results(browser, 'Event_Detection', results)
# Plot results
self.show_events(data, np.array(self.xOnsets), np.array(self.yOnsets),
dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
def func(self, browser):
""" Calculate the probability of having an event per time bin
Very simple threshold crossing event detection.
Options:
1) Threshold for detecting spikes
2) Time bin size (ms)
3) Event direction
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
try:
timeBin = np.abs(float(self.timeBin.text()))
except ValueError:
aux.error_box('Invalid time bin')
return
direction = str(self.eventDirection.currentText())
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Detect events in each trace
if direction == 'negative':
comp = lambda a, b: a < b
elif direction == 'positive':
comp = lambda a, b: a > b
# Check time bin (using the first plotted item)
item = plotWidget.plotDataItems[0]
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
if (timeBin / dt == 0) or (len(data) < timeBin / dt):
aux.error_box(
'Invalid time bin',
infoText=
'Make sure time bin is smaller than the selected data range')
return
# Detect events
results = []
plotWidget.clear()
for item in plotWidget.plotDataItems:
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
apCounter, i = 0, 0
xOnsets, yOnsets = [], []
while i < len(data):
if comp(data[i], threshold):
xOnsets.append(i)
yOnsets.append(data[i])
apCounter += 1
while i < len(data) and comp(data[i], threshold):
i += 1 # skip values if index in bounds AND until the value is below/above threshold again
else:
i += 1
# Get events per time bin
binSize = int(timeBin / dt)
nbins = np.ceil(len(data) / binSize)
eventCounter = []
for b in np.arange(1, nbins + 1):
count = np.sum((xOnsets > (b - 1) * binSize)
& (xOnsets < (b * binSize)))
eventCounter.append(count)
bins = np.arange(0 + binSize / 2., nbins * binSize + binSize / 2.,
binSize) * dt
# Store data
results.append(['event_counts', np.array(eventCounter)])
# Plot detected events
self.show_events(data, np.array(xOnsets), np.array(yOnsets), dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
# Store results
results.append(['time_bins', bins])
aux.save_results(browser, parentText + '_eventProbability', results)
def func(self, browser):
""" Measure selected properties or statistics in the region defined
by the data cursors.
Rise time and onset are calculated by finding the peak and walking
back until the limits are crossed. Onset limit is baseline mean; if
no baseline has been set, it is taken as the mean value of the first
1 ms of data.
Options:
1) create new entries in Working Data tree with the results
"""
############################################
# ANALYSIS FUNCTION
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Replot data to clear previous measure plot points
pgplot.replot(browser, plotWidget)
# Iterate through traces
dataMin, dataMax, dataMean, dataMedian, dataSEM = [], [], [], [], []
dataRiseTime, dataOnset, dataDecay = [], [], []
for item in plotWidget.plotDataItems:
# Get dt and data range
dt = item.attrs['dt']
data, c1, cx1, cx2 = aux.get_dataRange(plotWidget, item, cursors=True)
# Check baseline
if 'baselineStart' in item.analysis:
bsl = 0 # the mean of the baseline will always be 0
else:
bsl = np.mean(data[0:round(1./dt)])
# Measure selected parameters
if self.minBox.isChecked():
y = np.min(data)
x = np.argmin(data)
dataMin.append(y)
aux.plot_point(plotWidget, c1, x, y, dt)
if self.maxBox.isChecked():
y = np.max(data)
x = np.argmax(data)
dataMax.append(y)
aux.plot_point(plotWidget, c1, x, y, dt)
if self.meanBox.isChecked():
y = np.mean(data)
dataMean.append(y)
plotWidget.plot([cx1,cx2], [y,y], pen=pg.mkPen('#CF1C04', width=1))
if self.medianBox.isChecked():
y = np.median(data)
dataMedian.append(y)
plotWidget.plot([cx1,cx2], [y,y], pen=pg.mkPen('#CF1C04', width=1))
if self.semBox.isChecked():
y = np.std(data)/np.sqrt(len(data))
dataSEM.append(y)
plotWidget.plot([cx1,cx2], [y,y], pen=pg.mkPen('#CF1C04', width=1))
if self.riseTimeBox.isChecked():
try:
lowerLimit = float(self.riseLowerLimit.text())/100
upperLimit = float(self.riseUpperLimit.text())/100
except ValueError:
aux.error_box('Invalid limits')
return
# Get peak
xPeak, yPeak = self.get_peak(data)
# Get limits
lowerLimit = lowerLimit*(yPeak-bsl)+bsl
upperLimit = upperLimit*(yPeak-bsl)+bsl
# Find limit crosses
lowerCrossed, upperCrossed = False, False
i = 0
while lowerCrossed==False or upperCrossed==False:
if (upperCrossed==False) and self.comp(data[xPeak-i],upperLimit):
xUpper = xPeak-i
upperCrossed = True
if self.comp(data[xPeak-i], lowerLimit):
xLower = xPeak-i
lowerCrossed = True
i+=1
dataRiseTime.append((xUpper-xLower)*dt)
# Plot points
aux.plot_point(plotWidget, c1, xLower, lowerLimit, dt)
aux.plot_point(plotWidget, c1, xUpper, upperLimit, dt)
if self.onsetBox.isChecked():
xPeak, yPeak = self.get_peak(data)
bslCrossed = False
i = 0
while bslCrossed==False:
if self.comp(data[xPeak-i], bsl):
onset = xPeak-i
bslCrossed = True
i+=1
aux.plot_point(plotWidget, c1, onset, bsl, dt)
dataOnset.append(onset*dt)
if self.decayTimeBox.isChecked():
try:
decayLimit = float(self.decayLimit.text())/100
except ValueError:
aux.error_box('Invalid limits')
return
xPeak, yPeak = self.get_peak(data)
yDecay = decayLimit*(yPeak-bsl)+bsl
decayCrossed = False
i = 0
while decayCrossed==False:
if self.comp(data[xPeak+i], yDecay):
decayTime = xPeak+i
decayCrossed = True
i+=1
aux.plot_point(plotWidget, c1, decayTime, yDecay, dt)
dataDecay.append(decayTime*dt)
# Store results
results = []
if self.storeBox.isChecked():
if self.minBox.isChecked(): results.append(['Minimum', np.array(dataMin)])
if self.maxBox.isChecked(): results.append(['Maximum', np.array(dataMax)])
if self.meanBox.isChecked(): results.append(['Mean', np.array(dataMean)])
if self.medianBox.isChecked(): results.append(['Median', np.array(dataMedian)])
if self.semBox.isChecked(): results.append(['SEM', np.array(dataSEM)])
if self.riseTimeBox.isChecked(): results.append(['RiseTime', np.array(dataRiseTime)])
if self.onsetBox.isChecked(): results.append(['Onset', np.array(dataOnset)])
if self.decayTimeBox.isChecked(): results.append(['Decay', np.array(dataDecay)])
aux.save_results(browser, 'Measurements', results)
def func(self, browser):
""" Generate a FI curve from current steps
Options:
1) Threshold for detecting spikes
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Detect APs in each trace
comp = lambda a, b: a > b
apNumber, apFrequency, results = [], [], []
plotWidget.clear()
for item in plotWidget.plotDataItems:
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
apCounter, i = 0, 0
xOnsets, yOnsets = [], []
while i<len(data):
if comp(data[i],threshold):
xOnsets.append(i)
yOnsets.append(data[i])
apCounter+=1
while i<len(data) and comp(data[i],threshold):
i+=1 # skip values if index in bounds AND until the value is below/above threshold again
else:
i+=1
# Calculate AP frequency as 1/mean(ISI)
isi = np.mean(np.diff(xOnsets))*dt # in ms
if isi>0:
freq = 1/(isi/1000.)
else:
freq = 0.0
# Store number of APs and mean frequency
apNumber.append(apCounter)
apFrequency.append(freq)
# Plot detected APs
self.show_events(data, np.array(xOnsets), np.array(yOnsets), dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
# Store results
results.append(['AP_number', np.array(apNumber)])
results.append(['AP_frequency', np.array(apFrequency)])
aux.save_results(browser, parentText+'_FI', results)
def func(self, browser):
""" Fit data traces within cursor-defined range
Options:
1) Equation
2) Initial guesses
"""
############################################
# ANALYSIS FUNCTION
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Replot data to clear previous measure plot points
pgplot.replot(browser, plotWidget)
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Get current function
currentFuncmap = self.dataFit.fitfuncmap[str(self.comboBox.currentText())]
# Read initial guesses
pInit = []
try:
nParam = len(currentFuncmap[2])
for n in range(nParam): pInit.append(float(self.p[n].text()))
except ValueError:
aux.error_box('Invalid value in initial guess')
return
# Fit data
fitResults, fitTraces, fitTracesAttrs = [], [], []
for item in plotWidget.plotDataItems:
# Get data range to fit
dt = item.attrs['dt']
fitTracesAttrs.append(item.attrs)
yData, c1, cx1, cx2 = aux.get_dataRange(plotWidget, item, cursors=True)
xRange = pgplot.make_xvector(yData, dt)+cx1
self.dataFit.c1 = cx1
# Fit
func = currentFuncmap[0]
fitParams = self.dataFit.fit(func, xRange, yData, pInit)
fitResults.append(fitParams)
print fitParams
# Plot fitted function over trace
if self.extendBox.isChecked():
xRange = pgplot.make_xvector(item.data, dt)
#xRange = np.arange(plotWidget.viewBox.viewRange()[0][0], plotWidget.viewBox.viewRange()[0][1], dt)
fittedTrace = func(xRange, *fitParams)
plotWidget.plot(xRange, fittedTrace, pen=pg.mkPen('r', width=1))
fitTraces.append(fittedTrace)
# Store results
if self.storeBox.isChecked():
fitResults = np.array(fitResults)
results = []
for n in range(np.shape(fitResults)[1]):
results.append([str(self.plabels[n].text()), fitResults[:,n]])
for n in range(len(fitTraces)):
results.append(['fitTraces_'+str(n), fitTraces[n], fitTracesAttrs[n]])
aux.save_results(browser, parentText+'_fit', results)
def func(self, browser):
""" Calculate the probability of having an event per time bin
Very simple threshold crossing event detection.
Options:
1) Threshold for detecting spikes
2) Time bin size (ms)
3) Event direction
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
try:
timeBin = np.abs(float(self.timeBin.text()))
except ValueError:
aux.error_box('Invalid time bin')
return
direction = str(self.eventDirection.currentText())
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Detect events in each trace
if direction=='negative':
comp = lambda a, b: a < b
elif direction=='positive':
comp = lambda a, b: a > b
# Check time bin (using the first plotted item)
item = plotWidget.plotDataItems[0]
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
if (timeBin/dt==0) or (len(data)<timeBin/dt):
aux.error_box('Invalid time bin', infoText='Make sure time bin is smaller than the selected data range')
return
# Detect events
results = []
plotWidget.clear()
for item in plotWidget.plotDataItems:
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
apCounter, i = 0, 0
xOnsets, yOnsets = [], []
while i<len(data):
if comp(data[i],threshold):
xOnsets.append(i)
yOnsets.append(data[i])
apCounter+=1
while i<len(data) and comp(data[i],threshold):
i+=1 # skip values if index in bounds AND until the value is below/above threshold again
else:
i+=1
# Get events per time bin
binSize = int(timeBin/dt)
nbins = np.ceil(len(data)/binSize)
eventCounter = []
for b in np.arange(1, nbins+1):
count = np.sum((xOnsets>(b-1)*binSize) & (xOnsets<(b*binSize)))
eventCounter.append(count)
bins = np.arange(0+binSize/2., nbins*binSize+binSize/2., binSize)*dt
# Store data
results.append(['event_counts', np.array(eventCounter)])
# Plot detected events
self.show_events(data, np.array(xOnsets), np.array(yOnsets), dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
# Store results
results.append(['time_bins', bins])
aux.save_results(browser, parentText+'_eventProbability', results)
def func(self, browser):
""" Get some properties of currently plotted tracking trigger events
extracted with behaviour_triggerEvents.py module
Properties measured:
1 - failures to escape
2 - latency to escape
3 - time to reach the nest
4 - average speed of escape
5 - peak speed during escape
Extracted events have useful attributes:
t0 : data point of the trigger from the start of the event
trigger_time : data point of the trigger from the start of the original
tracking trace
Options:
1) Threshold for the nest long-axis coordinate
2) Threshold for the position derivative (to measure response latency)
"""
############################################
# ANALYSIS FUNCTION
# Read options
nestPos = float(self.plotWidget.nestCursorThsPos)
derivativeThs = float(self.plotWidget.derivativeCursorThsPos)
# Get plotted events
events = self.plotWidget.plotDataItems
# Go through events
failures = []
latencies, timeToNest, avgSpeed, maxSpeed = [], [], [], []
comp = lambda a, b: a < b
for event in events:
# Get data range
#data, c1 = aux.get_dataRange(plotWidget, event)
# Mark failures depending on position reached nest
if np.sum(event.data<nestPos)==0:
failures.append(1)
else:
failures.append(0)
# Get latency to reaction
t0 = event.attrs['t0']
i = t0 # start from stimulus trigger
dtrace = np.diff(event.data)
while i<len(dtrace):
if comp(dtrace[i], derivativeThs):
latencies.append(i-t0)
break
i+=1
# Get latency to nest
i = t0
while i<len(event.data):
if comp(event.data[i], nestPos):
timeToNest.append(i-t0)
break
i+=1
# Get other measures
avgSpeed.append(np.mean(dtrace[t0:i]))
maxSpeed.append(dtrace[t0:i].min())
# Store data
results = []
results.append(['Failures', failures])
results.append(['Latencies', latencies])
results.append(['Time_to_nest', timeToNest])
results.append(['Average_speed', avgSpeed])
results.append(['Max_speed', maxSpeed])
aux.save_results(self.browser, 'Event_measurements', results)
def func(self, browser):
""" Fit data traces within cursor-defined range
Options:
1) Equation
2) Initial guesses
"""
############################################
# ANALYSIS FUNCTION
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Replot data to clear previous measure plot points
pgplot.replot(browser, plotWidget)
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Get current function
currentFuncmap = self.dataFit.fitfuncmap[str(
self.comboBox.currentText())]
# Read initial guesses
pInit = []
try:
nParam = len(currentFuncmap[2])
for n in range(nParam):
pInit.append(float(self.p[n].text()))
except ValueError:
aux.error_box('Invalid value in initial guess')
return
# Fit data
fitResults, fitTraces, fitTracesAttrs = [], [], []
for item in plotWidget.plotDataItems:
# Get data range to fit
dt = item.attrs['dt']
fitTracesAttrs.append(item.attrs)
yData, c1, cx1, cx2 = aux.get_dataRange(plotWidget,
item,
cursors=True)
xRange = pgplot.make_xvector(yData, dt) + cx1
self.dataFit.c1 = cx1
# Fit
func = currentFuncmap[0]
fitParams = self.dataFit.fit(func, xRange, yData, pInit)
fitResults.append(fitParams)
print fitParams
# Plot fitted function over trace
if self.extendBox.isChecked():
xRange = pgplot.make_xvector(item.data, dt)
#xRange = np.arange(plotWidget.viewBox.viewRange()[0][0], plotWidget.viewBox.viewRange()[0][1], dt)
fittedTrace = func(xRange, *fitParams)
plotWidget.plot(xRange, fittedTrace, pen=pg.mkPen('r', width=1))
fitTraces.append(fittedTrace)
# Store results
if self.storeBox.isChecked():
fitResults = np.array(fitResults)
results = []
for n in range(np.shape(fitResults)[1]):
results.append([str(self.plabels[n].text()), fitResults[:, n]])
for n in range(len(fitTraces)):
results.append(
['fitTraces_' + str(n), fitTraces[n], fitTracesAttrs[n]])
aux.save_results(browser, parentText + '_fit', results)
def func(self, browser):
""" Generate a FI curve from current steps
Options:
1) Threshold for detecting spikes
"""
############################################
# ANALYSIS FUNCTION
# Read detection options
try:
threshold = float(self.browser.ui.dataPlotsWidget.cursorThsPos)
except NameError:
aux.error_box('No threshold selected')
return
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Detect APs in each trace
comp = lambda a, b: a > b
apNumber, apFrequency, results = [], [], []
plotWidget.clear()
for item in plotWidget.plotDataItems:
dt = item.attrs['dt']
data, c1 = aux.get_dataRange(plotWidget, item)
apCounter, i = 0, 0
xOnsets, yOnsets = [], []
while i < len(data):
if comp(data[i], threshold):
xOnsets.append(i)
yOnsets.append(data[i])
apCounter += 1
while i < len(data) and comp(data[i], threshold):
i += 1 # skip values if index in bounds AND until the value is below/above threshold again
else:
i += 1
# Calculate AP frequency as 1/mean(ISI)
isi = np.mean(np.diff(xOnsets)) * dt # in ms
if isi > 0:
freq = 1 / (isi / 1000.)
else:
freq = 0.0
# Store number of APs and mean frequency
apNumber.append(apCounter)
apFrequency.append(freq)
# Plot detected APs
self.show_events(data, np.array(xOnsets), np.array(yOnsets), dt)
# Turn cursors off (the plot has been cleared so there are no cursors displayed)
self.browser.ui.actionShowCursors.setChecked(False)
plotWidget.cursor = False
# Store results
results.append(['AP_number', np.array(apNumber)])
results.append(['AP_frequency', np.array(apFrequency)])
aux.save_results(browser, parentText + '_FI', results)
def func(self, browser):
""" Measure selected properties or statistics in the region defined
by the data cursors.
Rise time and onset are calculated by finding the peak and walking
back until the limits are crossed. Onset limit is baseline mean; if
no baseline has been set, it is taken as the mean value of the first
1 ms of data.
Options:
1) create new entries in Working Data tree with the results
"""
############################################
# ANALYSIS FUNCTION
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Replot data to clear previous measure plot points
pgplot.replot(browser, plotWidget)
# Iterate through traces
dataMin, dataMax, dataMean, dataMedian, dataSEM = [], [], [], [], []
dataRiseTime, dataOnset, dataDecay = [], [], []
for item in plotWidget.plotDataItems:
# Get dt and data range
dt = item.attrs['dt']
data, c1, cx1, cx2 = aux.get_dataRange(plotWidget,
item,
cursors=True)
# Check baseline
if 'baselineStart' in item.analysis:
bsl = 0 # the mean of the baseline will always be 0
else:
bsl = np.mean(data[0:round(1. / dt)])
# Measure selected parameters
if self.minBox.isChecked():
y = np.min(data)
x = np.argmin(data)
dataMin.append(y)
aux.plot_point(plotWidget, c1, x, y, dt)
if self.maxBox.isChecked():
y = np.max(data)
x = np.argmax(data)
dataMax.append(y)
aux.plot_point(plotWidget, c1, x, y, dt)
if self.meanBox.isChecked():
y = np.mean(data)
dataMean.append(y)
plotWidget.plot([cx1, cx2], [y, y],
pen=pg.mkPen('#CF1C04', width=1))
if self.medianBox.isChecked():
y = np.median(data)
dataMedian.append(y)
plotWidget.plot([cx1, cx2], [y, y],
pen=pg.mkPen('#CF1C04', width=1))
if self.semBox.isChecked():
y = np.std(data) / np.sqrt(len(data))
dataSEM.append(y)
plotWidget.plot([cx1, cx2], [y, y],
pen=pg.mkPen('#CF1C04', width=1))
if self.riseTimeBox.isChecked():
try:
lowerLimit = float(self.riseLowerLimit.text()) / 100
upperLimit = float(self.riseUpperLimit.text()) / 100
except ValueError:
aux.error_box('Invalid limits')
return
# Get peak
xPeak, yPeak = self.get_peak(data)
# Get limits
lowerLimit = lowerLimit * (yPeak - bsl) + bsl
upperLimit = upperLimit * (yPeak - bsl) + bsl
# Find limit crosses
lowerCrossed, upperCrossed = False, False
i = 0
while lowerCrossed == False or upperCrossed == False:
if (upperCrossed == False) and self.comp(
data[xPeak - i], upperLimit):
xUpper = xPeak - i
upperCrossed = True
if self.comp(data[xPeak - i], lowerLimit):
xLower = xPeak - i
lowerCrossed = True
i += 1
dataRiseTime.append((xUpper - xLower) * dt)
# Plot points
aux.plot_point(plotWidget, c1, xLower, lowerLimit, dt)
aux.plot_point(plotWidget, c1, xUpper, upperLimit, dt)
if self.onsetBox.isChecked():
xPeak, yPeak = self.get_peak(data)
bslCrossed = False
i = 0
while bslCrossed == False:
if self.comp(data[xPeak - i], bsl):
onset = xPeak - i
bslCrossed = True
i += 1
aux.plot_point(plotWidget, c1, onset, bsl, dt)
dataOnset.append(onset * dt)
if self.decayTimeBox.isChecked():
try:
decayLimit = float(self.decayLimit.text()) / 100
except ValueError:
aux.error_box('Invalid limits')
return
xPeak, yPeak = self.get_peak(data)
yDecay = decayLimit * (yPeak - bsl) + bsl
decayCrossed = False
i = 0
while decayCrossed == False:
if self.comp(data[xPeak + i], yDecay):
decayTime = xPeak + i
decayCrossed = True
i += 1
aux.plot_point(plotWidget, c1, decayTime, yDecay, dt)
dataDecay.append(decayTime * dt)
# Store results
results = []
if self.storeBox.isChecked():
if self.minBox.isChecked():
results.append(['Minimum', np.array(dataMin)])
if self.maxBox.isChecked():
results.append(['Maximum', np.array(dataMax)])
if self.meanBox.isChecked():
results.append(['Mean', np.array(dataMean)])
if self.medianBox.isChecked():
results.append(['Median', np.array(dataMedian)])
if self.semBox.isChecked():
results.append(['SEM', np.array(dataSEM)])
if self.riseTimeBox.isChecked():
results.append(['RiseTime', np.array(dataRiseTime)])
if self.onsetBox.isChecked():
results.append(['Onset', np.array(dataOnset)])
if self.decayTimeBox.isChecked():
results.append(['Decay', np.array(dataDecay)])
aux.save_results(browser, 'Measurements', results)
def func(self, browser):
""" Filter traces
Options:
1) Filter type (currently Bessel only)
2) Filter parameters
Note: filter frequencies are in Hz, make sure dt is in seconds
"""
############################################
# ANALYSIS FUNCTION
# Get options
btype = str(self.comboPass.currentText())
if 'Low' in btype:
btype = 'low'
elif 'High' in btype:
btype = 'high'
try:
cutoff = float(self.filterCutoff.text())
order = float(self.filterOrder.text())
except ValueError:
aux.error_box('Invalid Cut off or Order value')
return
bidir = self.filterDirection.isChecked()
# Get widgets
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
# Get parent text of plotted items
try:
parentText = plotWidget.plotDataItems[0].parent().text(
0) # Assumes all plotted data have the same parent
except AttributeError: # Parent = None
parentText = 'Data'
# Filter data
results, itemsToPlot = [], []
for item in plotWidget.plotDataItems:
# Copy attributes and add some new ones
attrs = item.attrs
attrs['filter_type'] = btype
attrs['filter_cutoff'] = cutoff
attrs['filter_order'] = order
# Filter
traceFilter = acq4filter.besselFilter(
item.data, cutoff, order,
float(item.attrs['dt']) / 1000, btype, bidir)
results.append([item.text(0), traceFilter, attrs])
# Store filtered traces
filterItem = aux.make_h5item('filter', traceFilter, item.attrs)
itemsToPlot.append(filterItem)
# Plot results
pgplot.plot_multipleData(browser,
plotWidget,
itemsToPlot,
clear=False,
color='#F2EF44')
# Store results
aux.save_results(browser, parentText + '_filter', results)
def func(self, browser):
""" Calculate average trace from currently plotted traces. If cursors are
selected the average is calculated for the range within the cursors.
Options:
1) create new entry in Working Data tree with the result
2) plot average with orginal traces
3) caclulate SD and SEM
"""
############################################
# ANALYSIS FUNCTION
plotWidget = browser.ui.dataPlotsWidget
toolsWidget = browser.ui.oneDimToolStackedWidget
results = []
# Get data and cursors
data = []
for item in plotWidget.plotDataItems:
dt = item.attrs['dt']
dataRange, c1 = aux.get_dataRange(plotWidget, item)
data.append(dataRange)
data = np.array(data)
# Calculate average and make h5item for plotting
try:
#avgData = np.nanmean(data[:, c1:c2], 0)
avgData = np.mean(data, 0)
avgItem = aux.make_h5item('avg', avgData, plotWidget.plotDataItems[0].attrs)
results.append(['avg_trace', avgData, item.attrs])
except ValueError:
aux.error_box('Cannot calculate average on data with different lengths', sys.exc_info(),
'Please ensure that all traces have the same length')
return
# Calculate SD and SEM
if self.sdBox.isChecked():
#sdData = np.nanstd(data[:, c1:c2], 0)
sdData = np.std(data, 0)
avgPlusSDItem = aux.make_h5item('avg+sd', avgData+sdData, plotWidget.plotDataItems[0].attrs)
avgMinusSDItem = aux.make_h5item('avg-sd', avgData-sdData, plotWidget.plotDataItems[0].attrs)
results.append(['avg+sd', avgData+sdData, item.attrs])
results.append(['avg-sd', avgData-sdData, item.attrs])
if self.semBox.isChecked():
#semData = np.nanstd(data[:, c1:c2], 0)/np.sqrt(len(data))
semData = np.std(data, 0)/np.sqrt(len(data))
avgPlusSEMItem = aux.make_h5item('avg+sem', avgData+semData, plotWidget.plotDataItems[0].attrs)
avgMinusSEMItem = aux.make_h5item('avg-sem', avgData-semData, plotWidget.plotDataItems[0].attrs)
results.append(['avg+sem', avgData+semData, item.attrs])
results.append(['avg-sem', avgData-semData, item.attrs])
# Plot data
if self.showTraces.isChecked():
clear = False
else:
clear = True
pgplot.browse_singleData(browser, plotWidget, avgItem, clear=clear, color='r')
# Store data
if self.storeResult.isChecked():
aux.save_results(browser, item.parent().text(0)+'_average', results)