from jaratest.nick.database import dataloader
from jaratest.nick.database import dataplotter
from jaratest.nick.database import cellDB
from jaratest.nick.database import clusterfuncs
from jaratoolbox import spikesorting
from matplotlib import pyplot as plt
from jaratoolbox import behavioranalysis
from jaratoolbox import spikesanalysis
reload(cellDB)
reload(clusterfuncs)
figdb = cellDB.CellDB()
figdbFn = '/home/nick/data/database/pinp003_thalamus_cells.json'
figdb.load_from_json(figdbFn)
loader = dataloader.DataLoader('offline', experimenter='nick')
figdb[0].get_session_types()
clusterfuncs.plot_cluster_tuning(figdb[1], 3)
spikeData, eventData, behavData = loader.get_cluster_data(figdb[1], 3)
currentFreq = behavData['currentFreq']
possibleFreq = np.unique(currentFreq)
currentIntensity = behavData['currentIntensity']
possibleIntensity = np.unique(currentIntensity)
spikeTimestamps = spikeData.timestamps
eventOnsetTimes = loader.get_event_onset_times(eventData)
from jaratest.nick.database import cellDB
dbFn = '/home/nick/data/database/nick_thalamus_cells.json'
db = cellDB.CellDB()
db.load_from_json(dbFn)
figuredb = cellDB.CellDB()
figuredb.append(db[0])
figuredb.append(db[8])
figuredb.append(db[10])
figuredb.append(db[1])
figuredb[0].comments='B/C/D Option - site 1 T6c3 (Thalamus)'
figuredb[1].comments='B/C/D (our favorite so far), also possibly J - site 6 T6c3 (Thalamus)'
figuredb[2].comments='J - site4 T3c10 (Thalamus)'
figuredb[3].comments='K - site1 T6c6 (Thalamus)'
cortexFn = '/home/nick/Desktop/cortexdb.json'
cortexdb = cellDB.CellDB()
cortexdb.load_from_json(cortexFn)
for cell in cortexdb:
figuredb.append(cell)
def setUp(self):
self.database = cellDB.CellDB()
d2site1.add_session('11-15-56', None, sessionTypes['nb'])
d2site1.add_session('11-18-36', None, sessionTypes['lp'])
d2site1.add_session('11-21-26', None, sessionTypes['lt'])
d2site1.add_session('11-25-58', 'a', sessionTypes['tc'])
d2site1.add_session('11-39-46', None, sessionTypes['bf'])
d2site1.add_session('11-42-37', None, sessionTypes['3p'])
d2site1.add_session('11-45-22', None, sessionTypes['1p'])
d2site1.add_clusters({3: [2, 3, 5], 6:[3, 7]})
# ----------------------
##Initializing the database and adding clusters
# ----------------------
db = cellDB.CellDB()
db.add_clusters(d1site1.clusterList)
db.add_clusters(d2site1.clusterList)
# ----------------------
##Saving and loading databases
# ----------------------
#Writing currently overwrites the file. The proper way is to load the database,
#append new clusters to it, and then rewrite the file with the new contents added
#However, I am currently asking for confirmation unless you pass force=True.
dbfile = '/tmp/allcells.json'
db.write_to_json(dbfile)