'''
List of all isolated units from adap015, with cluster quality added.
Lan Guo 2016-03-25
'''
#using CellDatabase that contains laserSession for evaluating laser responsiveness
from jaratoolbox.test.lan.Ephys import celldatabase_quality_vlan as celldatabase
reload(celldatabase)
eSession = celldatabase.EphysSessionInfo # Shorter name to simplify code
cellDB = celldatabase.CellDatabase()
oneES = eSession(animalName='adap015',
ephysSession='2016-02-04_15-41-31',
clustersEachTetrode={
1: range(1, 13),
2: range(1, 13),
3: range(1, 13),
4: range(1, 13),
5: range(1, 13),
6: range(1, 13),
7: range(1, 13),
8: range(1, 13)
},
behavSession='20160204a',
clusterQuality={
1: [3, 4, 2, 4, 4, 3, 3, 2, 1, 4, 4, 4],
2: [3, 1, 3, 2, 1, 2, 6, 2, 6, 6, 2, 0],
3: [3, 1, 1, 1, 4, 1, 1, 1, 3, 0, 0, 0],
4: [3, 2, 2, 1, 1, 2, 4, 4, 1, 1, 1, 0],
countTimeRange = [float(sys.argv[2]),float(sys.argv[3])]
#second and third argument are numbers specify the start and end of countTimeRange in seconds, e.g. 0 0.1
subjectList = sys.argv[4:] #the fourth argument onwards are the mouse names to tell the script which allcells file to use
for subject in subjectList:
allcellsFileName = 'allcells_'+subject
sys.path.append(settings.ALLCELLS_PATH)
allcells = importlib.import_module(allcellsFileName)
numOfCells = len(allcells.cellDB) #number of cells that were clustered on all sessions clustered
outputDir = '/home/languo/data/ephys/'+subject+'/'
CellInfo = celldatabase.CellInfo #This is for creating subdatabase for responsive and modulated cells
responsiveCellDB = celldatabase.CellDatabase()
modulatedCellDB = celldatabase.CellDatabase()
allCellDB= celldatabase.CellDatabase()
###################Choose alignment and time window to plot mod Index histogram#######################
processedDir = os.path.join(outputDir,subject+'_stats')
#alignment = 'side-in'#put here alignment choice!!choices are 'sound', 'center-out', 'side-in'.
#countTimeRange = [-0.1,0]
window = str(countTimeRange[0])+'to'+str(countTimeRange[1])+'sec_window_'
nameOfmodSFile = 'modSig_'+alignment+'_'+window+subject+'.txt'
nameOfmodIFile = 'modIndex_'+alignment+'_'+window+subject+'.txt'
modIFilename = os.path.join(processedDir,nameOfmodIFile)
modSFilename = os.path.join(processedDir,nameOfmodSFile)
#############################################################################
checkLaserResponse = 0
#######################################################################
for subject in subjectList:
allcellsFileName = 'allcells_' + subject
sys.path.append(settings.ALLCELLS_PATH)
allcells = importlib.import_module(allcellsFileName)
numOfCells = len(
allcells.cellDB
) #number of cells that were clustered on all sessions clustered
print numOfCells
fullOutputDir = '/home/languo/data/ephys/' + subject + '/' + subject + '_stats'
allCellDB = allcells.cellDB
modulatedCellDB = celldatabase.CellDatabase()
if checkLaserResponse:
sigModFilename = 'sigMod_' + alignment + '_' + window + 'ISIchecked_laserResponsive'
else:
sigModFilename = 'sigMod_' + alignment + '_' + window + 'ISIchecked'
try:
sigModI_file = open('%s/%s.txt' % (fullOutputDir, sigModFilename), 'r')
for line in sigModI_file:
cellID = int(line.split(':')[1].split()[0])
modulatedCellDB.append(allCellDB[cellID])
sigModI_file.close()
except:
print sigModFilename + ' does not exist.'
continue
countTimeRange = [float(sys.argv[2]),int(sys.argv[3])]
else:
countTimeRange = [float(sys.argv[2]),float(sys.argv[3])]
for subject in subjectList:
allcellsFileName = 'allcells_'+subject
sys.path.append(settings.ALLCELLS_PATH)
allcells = importlib.import_module(allcellsFileName)
numOfCells = len(allcells.cellDB) #number of cells that were clustered on all sessions clustered
outputDir = '/home/languo/data/ephys/'+subject+'/'
CellInfo = celldatabase.CellInfo #This is for creating subdatabase for responsive and modulated cells
responsiveCellDB = celldatabase.CellDatabase()
soundnlaserResponsiveCellDB = celldatabase.CellDatabase()
modulatedCellDB = celldatabase.CellDatabase()
laserResponsiveCellDB = celldatabase.CellDatabase()
allCellDB= celldatabase.CellDatabase()
###################Choose alignment and time window to plot mod Index histogram.Also decide whether to check laser response###########
processedDir = os.path.join(outputDir,subject+'_stats')
#lignment = 'sound'
#put here alignment choice!!choices are 'sound', 'center-out', 'side-in'.
#ountTimeRange = [0,0.15]
window = str(countTimeRange[0])+'to'+str(countTimeRange[1])+'sec_window_'
checkLaserResponse=1 ####Whether to check laser response
########################################################################
sys.path.append(settings.ALLCELLS_PATH)
allcells = importlib.import_module(allcellsFileName)
numOfCells = len(
allcells.cellDB
) #number of cells that were clustered on all sessions clustered
outputDir = '/home/languo/data/ephys/' + subject + '/'
#binWidth = 0.020 # Size of each bin in histogram in seconds
clusNum = 12 #Number of clusters that Klustakwik speparated into
numTetrodes = 8 #Number of tetrodes
#CellInfo = celldatabase.CellInfo
LaserResponsiveCellDB = celldatabase.CellDatabase()
################################################################################################
##############################-----Minimum Requirements------###################################
################################################################################################
qualityList = [1, 6]
minZVal = 2.0
#maxISIviolation = 0.02
minPValue = 0.05
################################################################################################
################################################################################################
subject = allcells.cellDB[0].animalName
behavSession = ''
processedDir = os.path.join(outputDir, subject + '_stats')
maxZLaserFilename = os.path.join(processedDir,
sys.path.append(settings.ALLCELLS_PATH)
allcells = importlib.import_module(allcellsFileName)
numOfCells = len(
allcells.cellDB
) #number of cells that were clustered on all sessions clustered
outputDir = '/home/languo/data/ephys/' + subject + '/'
binWidth = 0.020 # Size of each bin in histogram in seconds
clusNum = 12 #Number of clusters that Klustakwik speparated into
numTetrodes = 8 #Number of tetrodes
CellInfo = celldatabase.CellInfo #This is for creating subdatabase for responsive and modulated cells
soundResponsiveCellDB = celldatabase.CellDatabase()
laserResponsiveCellDB = celldatabase.CellDatabase()
modulatedCellDB = celldatabase.CellDatabase()
modulatedCellDB_laser = celldatabase.CellDatabase()
################################################################################################
##############################-----Minimum Requirements------###################################
################################################################################################
qualityList = [1, 6] #[1,4,5,6,7]#range(1,10)
minZVal = 3.0
#maxISIviolation = 0.02
minPValue = 0.05
################################################################################################
################################################################################################
subject = allcells.cellDB[0].animalName
behavSession = ''