def PhaseVectors(doc, neurons, binSize):
'''
calculates instantaneous phase vectors for the given array of neurons
see PhaseArray above
'''
theStart = nex.GetDocStartTime(doc)
theEnd = nex.GetDocEndTime(doc)
numBins = np.int64(np.floor((theEnd - theStart) / binSize))
phaseVectors = []
for nr in neurons:
ts = nr.Timestamps()
if len(ts) == 0:
# no spikes, fill with random phases
phaseVectors.append(2 * np.pi * np.random.random(numBins))
continue
ts = np.array(ts) - theStart
# check if we need to add phantom spike at zero
if ts[0] > 0:
ts = np.insert(ts, 0, 0)
binIndexes = np.int64(np.floor(ts / binSize))
phaseVectors.append(PhaseArray(binIndexes, numBins))
return phaseVectors
def Histograms(doc, neurons, binSize):
'''
Calculates normalized rate histograms
formula (1) in Li [2007], where Z is the rate histogram
'''
theStart = nex.GetDocStartTime(doc)
theEnd = nex.GetDocEndTime(doc)
theBins = np.arange(theStart, theEnd, binSize)
hists = []
for nr in neurons:
ts = nr.Timestamps()
hist, b = np.histogram(ts, bins=theBins)
if len(ts) > 0:
hist = (hist - np.mean(hist)) / np.std(hist)
hists.append(hist)
return hists
def IntervalFilterVarIfNeeded(doc, var, pars):
selData = pars['Select Data']
theFilter = pars['Interval Filter']
if selData == 'All' and theFilter == 'None':
# no need to filter
return var
mainFrom = 0.0
mainTo = nex.GetDocEndTime(doc)
if selData == 'From Time Range':
mainFrom = float(pars['Select Data From (sec)'])
mainTo = float(pars['Select Data To (sec)'])
tempInt = nex.NewIntEvent(doc, 0)
nex.AddInterval(tempInt, mainFrom, mainTo)
if theFilter == 'None':
return nex.IntervalFilter(var, tempInt)
else:
tempInt1 = nex.IntAnd(tempInt, doc[theFilter])
return nex.IntervalFilter(var, tempInt1)
# # ################################## # 1. The path for where the results are saved destination = "C:/Users/earnestt/Desktop" # 2. The name of the template being applied: template = "coherence_4_tetrodes" # 3. The start time in seconds of the analysis window: start = 0 # 4. The end time in seconds of the analysis window: #To select the end of any document, you can use # end = nex.GetDocEndTime(doc) end = nex.GetDocEndTime(doc) # 5. The names of the interval variables to include; specify their names in this list: intervals = ['pre-cocaine', 'post-cocaine'] ##################################################### #moves to the specified director os.chdir(destination) #loop for creating a new folder #new directory name is the document title plus the name of the template used #if the name already exists, a number is added g = 1 basename = nex.GetDocTitle(doc) + " " + template + " with intervals"
#end = nex.GetDocEndTime(doc)
end = 3750
# 5. The bin size for analysis, in seconds:
#The bin size must be no larger than the analysis period (end-start)
binsize = 30
#####################################################
#Checks some conditions about the user input to make sure the analysis will run properly
#stops the program when there is an issue
if start >= end:
print "Starting point (start) must be before ending point (end)."
sys.exit()
if end > nex.GetDocEndTime(doc):
print "The entered end of analysis period is outside of the recording length."
sys.exit()
if binsize > (end - start):
print "Analysis bin (binsize) must be at least the size of the analysis period."
sys.exit()
#makes list of points where the start of a bin will be
#if the last point in bin_starts is too close to the end of the analysis window,
#there will not be enough data to have a full bin
#in this case, this bin is dropped so that each bin has an equal amount of data
bin_starts = []
c = start