def __init__(self, baseDir=None, probes=None, probeGen='3b'):
if baseDir is None:
self.dataDir = dataDir
else:
self.dataDir = baseDir
sync_file = glob.glob(
os.path.join(self.dataDir, '*' + ('[0-9]' * 18) + '.h5'))
self.sync_file = sync_file[0] if len(sync_file) > 0 else None
self.syncDataset = sync.Dataset(
self.sync_file) if self.sync_file is not None else None
if probes is None:
self.probes_to_analyze = probeIDs
else:
self.probes_to_analyze = probes
self.experimentDate = os.path.basename(self.dataDir)[:8]
self.probeGen = probeGen
if probeGen == '3b':
if datetime.datetime.strptime(self.experimentDate,
'%m%d%Y') < datetime.datetime(
2019, 3, 15):
fprobe = '4'
else:
fprobe = '3'
self.PXIDict = {
'A': 'slot2-probe1',
'B': 'slot2-probe2',
'C': 'slot2-probe3',
'D': 'slot3-probe1',
'E': 'slot3-probe2',
'F': 'slot3-probe' + fprobe
}
else:
self.PXIDict = None
def __init__(self, baseDir=None, probes=None, probeGen='3b'):
if baseDir is None:
self.dataDir = dataDir
else:
self.dataDir = baseDir
if probeGen == 'pipeline':
sync_file = glob.glob(os.path.join(self.dataDir, '*.sync'))
else:
sync_file = glob.glob(
os.path.join(self.dataDir, '*' + ('[0-9]' * 18) + '.h5'))
if len(sync_file) > 0:
if len(sync_file) > 1:
# get the last generated syncfile (assuming earlier were false starts)
ftime = []
for f in sync_file:
i = f.find('.')
ftime.append(
datetime.datetime.strptime(f[i - 6:i], '%H%M%S'))
self.sync_file = sync_file[ftime.index(max(ftime))]
else:
self.sync_file = sync_file[0]
else:
self.sync_file = None
self.syncDataset = sync.Dataset(
self.sync_file) if self.sync_file is not None else None
if probes is None:
self.probes_to_analyze = probeIDs
else:
self.probes_to_analyze = probes
self.experimentDate = os.path.basename(self.dataDir)[:8]
self.probeGen = probeGen
if probeGen == '3b':
if datetime.datetime.strptime(self.experimentDate,
'%m%d%Y') < datetime.datetime(
2019, 3, 15):
fprobe = '4'
else:
fprobe = '3'
self.PXIDict = {
'A': 'slot2-probe1',
'B': 'slot2-probe2',
'C': 'slot2-probe3',
'D': 'slot3-probe1',
'E': 'slot3-probe2',
'F': 'slot3-probe' + fprobe
}
else:
self.PXIDict = None
def loadFromHDF5(self, filePath=None):
fileIO.hdf5ToObj(self,filePath)
self.syncDataset = sync.Dataset(self.sync_file)
self.getBehaviorData()
self.getRFandFlashStimInfo()
ymin = rawData[channelsToPlot, samplesToPlot].min()
ymax = rawData[channelsToPlot, samplesToPlot].max()
for i, ch in enumerate(channelsToPlot):
ax = fig.add_subplot(len(channelsToPlot), 1, i + 1)
ax.plot(rawData[ch, samplesToPlot], 'k')
for side in ('right', 'top'):
ax.spines[side].set_visible(False)
ax.set_ylim([ymin, ymax])
ax.set_ylabel('uV')
if i == len(channelsToPlot) - 1:
ax.set_xlabel('Sample')
ax.set_title('ch ' + str(ch))
plt.tight_layout()
# sync data
syncDataset = sync.Dataset(syncFile)
probeEventsDir = os.path.join(
os.path.join(probeDataDir, 'events',
'Neuropix-PXI-' + pxiDict[probeLabel]), 'TTL_1')
# get barcodes from sync file
bRising, bFalling = get_sync_line_data(syncDataset, 'barcode')
bs_t, bs = ecephys.extract_barcodes_from_times(bRising, bFalling)
# get barcodes from ephys data
channel_states = np.load(os.path.join(probeEventsDir, 'channel_states.npy'))
event_times = np.load(os.path.join(probeEventsDir, 'event_timestamps.npy'))
beRising = event_times[channel_states > 0] / 30000.
beFalling = event_times[channel_states < 0] / 30000.
# plotPerformance(exps,label=reg,sessions=sessions,led=led)
#
syncFiles = []
while True:
f = fileIO.getFile('choose sync file',fileType='*.h5')
if f!='':
syncFiles.append(f)
else:
break
ledOnset = []
for i,(f,obj) in enumerate(zip(syncFiles,exps)):
syncDataset = sync.Dataset(f)
frameRising, frameFalling = probeSync.get_sync_line_data(syncDataset, 'vsync_stim')
vsyncTimes = frameFalling[1:] if frameFalling[0] < frameRising[0] else frameFalling
frameAppearTimes = vsyncTimes + obj.monitorLag/obj.frameRate
binWidth = 0.001
for laserInd,ch in enumerate((11,1)):
laserRising,laserFalling = probeSync.get_sync_line_data(syncDataset,channel=ch)
if len(laserRising)>0:
laserTrials = obj.laser==laserInd
ct = frameAppearTimes[obj.changeFrames[laserTrials & (obj.changeTrials | obj.catchTrials)].astype(int)]
fig = plt.figure(figsize=(6,6))
for j,(t,xlbl) in enumerate(zip((laserRising,laserFalling),('onset','offset'))):
timeFromChange = t[~obj.laserOnBeforeAbort[laserTrials]]-ct
if xlbl=='onset':