reload(dataloader) from jaratoolbox.test.nick.database import cellDB reload(cellDB) from jaratoolbox.test.nick.database import dataplotter from jaratoolbox import spikesorting from jaratoolbox.test.nick import clustercutting from pylab import * loader = dataloader.DataLoader('offline', experimenter='nick') dbFn = '/home/nick/data/database/nick_thalamus_cells.json' db = cellDB.CellDB() db.load_from_json(dbFn) c = db[0] spikeData, eventData, behavData = loader.get_cluster_data(c, 'tc_heatmap') spikeTimes = spikeData.timestamps eventOnsetTimes = loader.get_event_onset_times(eventData) currentFreq = behavData['currentFreq'] currentIntensity = behavData['currentIntensity'] trialsToPlot = currentIntensity==70 eventOnsetTimes=eventOnsetTimes[trialsToPlot] currentFreq = currentFreq[trialsToPlot] dataplotter.plot_raster(spikeTimes, eventOnsetTimes, sortArray=currentFreq)
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) db2 = cellDB.CellDB() db2.load_from_json(dbfile)
from jaratoolbox.test.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) amdbFn = '/home/nick/Desktop/amdatabase.json' amdb = cellDB.CellDB() amdb.load_from_json(amdbFn)