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,
Example #2
0
'''
List of all isolated units from adap017, with cluster quality added.
Lan Guo 2016-03-25
'''
#using CellDatabase that contains laserSession for evaluating laser responsiveness

from jaratest.lan.Ephys import celldatabase_quality_vlan as celldatabase
reload(celldatabase)

eSession = celldatabase.EphysSessionInfo  # Shorter name to simplify code

cellDB = celldatabase.CellDatabase()

oneES = eSession(animalName='adap017',
                 ephysSession='2016-03-16_17-49-15',
                 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='20160316a',
                 clusterQuality={
                     1: [3, 1, 2, 2, 2, 1, 4, 2, 3, 1, 4, 1],
                     2: [3, 4, 1, 7, 4, 4, 1, 3, 3, 2, 1, 1],
                     3: [3, 2, 4, 4, 4, 4, 2, 1, 2, 3, 1, 2],
                     4: [3, 3, 1, 4, 5, 2, 2, 1, 2, 2, 4, 1],
subjectList = 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()
    modulatedCellDB = celldatabase.CellDatabase()
    allCellDB = celldatabase.CellDatabase()

    ###################Choose alignment and time window to plot mod Index histogram#######################
    processedDir = os.path.join(outputDir, subject + '_stats')
    #alignment = 'center-out'
    #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'

    if alignment == 'center-out':
        nameOfmovementmodSFile = 'modSig_' + 'LvsR_movement_' + window + subject + '.txt'
Example #4
0
allcells = importlib.import_module(allcellsFileName)

numOfCells = len(
    allcells.cellDB
)  #number of cells that were clustered on all sessions clustered
print 'number of cells:', numOfCells

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
allCellDB = celldatabase.CellDatabase()
modulatedCellDB = 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 = ''
processedDir = os.path.join(outputDir, subject + '_stats')
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 = ''
Example #6
0
    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
    ########################################################################