def plot_time_report(clusterlist, animalName, sessionList, siteName):
'''
clusterlist in format [(tetrode, cluster), (tetrode, cluster), etc.]
#NOTE: I am here
'''
for indPair, (tetrode, cluster) in enumerate(clusterlist):
oneTT = cms.MultipleSessionsToCluster(animalName, sessionList, tetrode,
siteName)
oneTT.load_all_waveforms()
clusterFile = os.path.join(oneTT.clustersDir,
'Tetrode%d.clu.1' % oneTT.tetrode)
oneTT.set_clusters_from_file()
normSpikeCount = 0
spikeTimestamps = oneTT.timestamps[oneTT.clusters == cluster]
chunkStarts = []
chunkSpikeCounts = []
EPHYS_SAMPLING_RATE = 30000.0
#Get the start and end times of each session from the cont data
#Cont channel 31 was recorded for each sesssion
contFn = '109_CH31.continuous'
sessionLims = np.empty((len(sessionList), 2))
for indSession, session in enumerate(sessionList):
contFile = os.path.join(settings.EPHYS_PATH, animalName, session,
contFn)
dataCont = loadopenephys.DataCont(contFile)
dataCont.timestamps = dataCont.timestamps / EPHYS_SAMPLING_RATE
sessionLims[indSession, 0] = dataCont.timestamps[0]
sessionLims[indSession, 1] = dataCont.timestamps[-1]
for indLims, lims in enumerate(sessionLims):
#Break the session into 2 min segments and discard the last non-full segment
splits = np.arange(lims[0], lims[1], 120)
chunks = zip(splits, splits[1:])
for indChunk, chunk in enumerate(chunks):
spikesThisChunk = spikeTimestamps[(
(spikeTimestamps > chunk[0]) &
(spikeTimestamps < chunk[1]))]
chunkStarts.append(chunk[0])
chunkSpikeCounts.append(len(spikesThisChunk))
if indLims == 1:
normSpikeCount = len(spikesThisChunk)
plt.subplot2grid((3, 1), (indPair, 0))
timebase = np.array(chunkStarts) / 60.0
timebase = timebase - timebase[0]
spikeCounts = np.array(chunkSpikeCounts) / np.double(normSpikeCount)
plt.plot(timebase, spikeCounts, 'ko-', lw=2)
plt.hold(1)
plt.axvline(x=(sessionLims[1, 1] - sessionLims[0, 0]) / 60.0,
color='r',
lw=3)
plt.axhline(y=1, color='0.5', lw=1)
plt.ylabel('tt{}c{}'.format(tetrode, cluster))
plt.ylim([0, 2.5])
def get_session_cont(self, session, channel):
if self.mode=='online':
ephysSession = self.get_session_filename(session)
contFilename = os.path.join(self.onlineEphysPath, ephysSession, '109_CH{}.continuous'.format(channel))
elif self.mode=='offline': #The session should already be relative to the mouse
contFilename = os.path.join(settings.EPHYS_PATH, session, '109_CH{}.continuous'.format(channel))
contData=loadopenephys.DataCont(contFilename) #FIXME: Convert to mV?
return contData
def get_session_cont(self, sessionDir, channel):
contFilename = os.path.join(self.ephysPath, sessionDir,
'109_CH{}.continuous'.format(channel))
contData = loadopenephys.DataCont(contFilename) #FIXME: Convert to mV?
return contData
def test_cont_loading(self):
contFn = '100_CH11.continuous'
contFile = os.path.join(testDataDir, contFn)
contData = loadopenephys.DataCont(contFile)
plt.plot(contData.samples[:10000], '.-')
def butter_bandpass(lowcut, highcut, fs, order=5):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
b, a = butter(order, [low, high], btype='band')
return b, a
def butter_bandpass_filter(data, lowcut, highcut, fs, order=5):
b, a = butter_bandpass(lowcut, highcut, fs, order=order)
y = lfilter(b, a, data)
return y
subject = 'pinp001'
#ephysSession = '2015-03-22_17-13-54' # tuning
ephysSession = '2015-03-22_17-27-28' # laser
ephysRoot = os.path.join(settings.EPHYS_PATH, subject)
filename = os.path.join(ephysRoot, ephysSession, '109_CH11.continuous')
dc = loadopenephys.DataCont(filename)
fc = butter_bandpass_filter(dc.samples, 300, 6000, 30000)
x = 140000
plot(fc[x:x + 200000])
show()
#maprow = tetrode
#mapcol = channel
#meanTraceEachChannel(sessions, tetrode, channel, samples)
meanTraceEachChannel = np.empty((len(sessions), np.shape(channelMap)[0], np.shape(channelMap)[1], secondsEachTrace*EPHYS_SAMPLING_RATE))
#for indChan, channel in enumerate(channels):
colors = plt.cm.viridis(np.linspace(0, 1, len(sessions)))
for indSession, session in enumerate(sessions):
for (indr, indc), channel in np.ndenumerate(channelMap):
contFn = '100_CH{}.continuous'.format(channel)
fullContFile = os.path.join(settings.EPHYS_PATH, animalName, session, contFn)
fullEventFile = os.path.join(settings.EPHYS_PATH, animalName, session, 'all_channels.events')
contData = loadopenephys.DataCont(fullContFile)
#Multiply by 1000 and div by gain (*1000/5000)
contData.samples = contData.samples/5.0
#Load the events
eventData = loadopenephys.Events(fullEventFile)
eventData.timestamps = eventData.timestamps[((eventData.eventID==1) & (eventData.eventChannel==0))]
startTimestamp = contData.timestamps[0]
eventSampleNumbers = eventData.timestamps - startTimestamp
traces = np.empty((len(eventSampleNumbers), secondsEachTrace*EPHYS_SAMPLING_RATE))
for indSamp, sampNumber in enumerate(eventSampleNumbers):
trace = contData.samples[sampNumber:sampNumber + secondsEachTrace*EPHYS_SAMPLING_RATE]
trace = trace - trace[0]
traces[indSamp, :] = trace
meanTrace = np.mean(traces, axis = 0)
#To convert spikes to mV, you have to divide by the gain,
from jaratoolbox import loadopenephys
from jaratoolbox import spikesorting
import os
#Data filenames
ephysPath = '/home/nick/data/ephys/pinp013/'
ephysFn='2016-05-27_14-08-54'
contFn = os.path.join(ephysPath, ephysFn, '109_CH23.continuous')
spikesFn = os.path.join(ephysPath, ephysFn, 'Tetrode2.spikes')
#Load data
dataCont = loadopenephys.DataCont(contFn)
dataSpikes = loadopenephys.DataSpikes(spikesFn)
#Convert to microvolts
GAIN = 5000.0
SAMPLING_RATE=30000.0
timebase = np.arange(len(dataCont.samples))/SAMPLING_RATE
dataCont.samples = (dataCont.samples / GAIN) * 1000
dataSpikes.samples = ((dataSpikes.samples - 32768.0) / GAIN) * 1000.0
#Set clusters
clustersFile = os.path.join(ephysPath, '{}_kk'.format(ephysFn), 'Tetrode2.clu.1')
dataSpikes.set_clusters(clustersFile)
###eventTimes=ev.timestamps #/SAMPLING_RATE
eventOnsetTimes = events.timestamps[events.eventID == 1] # Stim onset
###eventOnsetTimes=eventOnsetTimes[:-1] # The last behavior trial is always started but never finishe
#channelsToPlot = [15,18]
channelsToPlot = [16, 17]
channelsToPlot = [3, 6, 11, 15, 19, 23]
nChannels = len(channelsToPlot)
clf()
for indc, channel in enumerate(channelsToPlot):
#filenameOnly = '109_CH15.continuous'
#filenameOnly = '109_CH18.continuous'
filenameOnly = '109_CH{0}.continuous'.format(channel)
#filenameOnly = '110_CH{0:02d}.continuous'.format(channel)
filename = os.path.join(dataDir, filenameOnly)
datacont = loadopenephys.DataCont(filename)
(lockedLFP, timeVec) = datacont.lock_to_event(eventOnsetTimes, timeRange)
subplot(nChannels, 1, indc + 1)
maxAbsVal = np.max(abs(lockedLFP), axis=1)
tooLarge = maxAbsVal > 6000
plot(timeVec, mean(lockedLFP[~tooLarge, :], axis=0))
#plot(timeVec,mean(lockedLFP,axis=0))
#plot(timeVec,mean(lockedLFP[100:200,:],axis=0))
###plot(tile(timeVec,(1,locked)),lockedLFP) # NOT FINISHED
ylim([-200, 80])
show()
if 0:
clf()
plot(datacont.samples[:10000], '-')
possibleIntensity = np.unique(intensityEachTrial)
#Get the event timestamps from openEphys
ev=loadopenephys.Events(event_filename)
evID=np.array(ev.eventID)
eventOnsetTimes=ev.timestamps[evID==1] #The timestamps of all of the stimulus onsets
#These are the active channels in this recording, sorted by tetrode
tetrodeChannels = np.array([[9, 10, 11, 12], [13, 14, 15, 16], [17, 18, 19, 20], [21, 22, 23, 24]])
#Get the continuous data
channel = 24 #The channel to plot
reference = 9 #Experimental: plotting without subtracting a reference made all channels look the same.
cont_filename = os.path.join(ephysDir, '109_CH{0}.continuous'.format(channel))
ref_filename = os.path.join(ephysDir, '109_CH{0}.continuous'.format(reference))
ephysData = loadopenephys.DataCont(cont_filename)
refData = loadopenephys.DataCont(ref_filename)
#Subtract the reference channel (not sure yet if this is a good thing to include.)
#ephysData.samples = ephysData.samples - refData.samples
#The ephys data starts with a positive nonzero timestamp, corresponding to the system time somehow.
#We need to subtract this from all timestamp values if we want to know what sample number to get.
startTimestamp = ephysData.timestamps[0]
#Preallocate an array in which to store the values of each mean trace
meanTraceEachSetting = np.empty((len(possibleIntensity), len(possibleFreq), secondsEachTrace*SAMPLING_RATE))
#Loop through the frequencies and intensities in the list of possible settings,
#extracting the trace after the presentation of each possible kind of stimulus.
for indFreq, currentFreq in enumerate(possibleFreq):