subjects = ['adap016', 'adap017', 'adap018', 'adap019', 'adap020'] elif CASE == 7: subjects = ['adap021', 'adap022', 'adap023', 'adap024', 'adap025'] elif CASE == 8: subjects = ['d1pi008', 'd1pi009', 'd1pi010', 'd1pi011', 'd1pi012'] elif CASE == 0: subjects = ['adap010'] figure(CASE) # subjects = ['test011','test015','test016','test017', 'test012','test013','test014','test018','test019','test020'] # subjects = ['test011','test015','test016','test017','test018'] # subjects = ['test050','test052','test053', # 'test055','test056','test057','test058','test059'] #sessions = '20150311a' try: behavioranalysis.behavior_summary( subjects, session, trialslim=[0, 1000], outputDir='/var/tmp/behavior_reports/') except: print 'Something is wrong with this session' raise pass ''' subjects = ['test011','test015','test016'] sessions = ['20150222a','20150223a'] behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/tmp/') '''
''' Show performance report for each animal Example (on how to run): python daily_behavior_summary.py 20150212 ''' from jaratoolbox import behavioranalysis from pylab import * import sys datestring = str(sys.argv[1]) print datestring sessions = datestring+'a' subjects = ['test089','adap004','test087','adap010','adap002']#['test059','test055','test053','test086'] figure() try: behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/home/billywalker/data/behavior_reports/') except: print 'Something is wrong with this session' pass
For Daily Behavior Monitoring. Loads behavior data from mounted jarahub/data/behavior for animals of interest, plot psychometric curve and dynamics data. ''' import sys # from jaratest.nick import behavioranalysis_vnick as behavioranalysis from jaratoolbox import behavioranalysis reload(behavioranalysis) # subjects = ['amod001', 'amod002', 'amod003', 'amod004', 'amod005'] # subjects = ['adap026', 'adap027', 'adap028', 'adap029', 'adap030', ] # subjects = ['adap021', 'adap022', 'adap023', 'adap024', 'adap025' ] # subjects = ['adap022', 'adap026', 'adap027', 'adap030'] #New muscimol animals # subjects = ['adap025', 'adap028', 'adap029'] subjects = ['adap029'] # sessions = ['20160711a', '20160712a', '20160713a', '20160714a', '20160715a', '20160716a', '20160718a','20160719a', '20160720a', '20160721a', '20160722a'] sessions = [ '20160718a', '20160719a', '20160720a', '20160721a', '20160722a', '20160723a', '20160725a', '20160726a', '20160727a', '20160728a', '20160729a' ] if len(sys.argv) > 1: sessions = sys.argv[1:] #sessions = input("Enter sessions (in a list of strings ['','']) to check behavior performance:") behavioranalysis.behavior_summary(subjects, sessions, trialslim=[0, 1000], outputDir='/home/nick/data/behavior_reports')
from jaratoolbox import loadbehavior from jaratoolbox import extraplots reload(extraplots) import numpy as np from pylab import * import matplotlib.pyplot as plt from statsmodels.stats.proportion import proportion_confint #Used to compute confidence interval for the error bars. from jaratoolbox import settings import sys animalName = 'test012' session = '20150106a' experimenter = 'santiago' paradigm = '2afc' behavioranalysis.behavior_summary(animalName,session) sys.exit() behavFile = loadbehavior.path_to_behavior_data(animalName,experimenter,paradigm,session) bdata = loadbehavior.FlexCategBehaviorData(behavFile) targetFrequency = bdata['targetFrequency'] choice=bdata['choice'] valid=bdata['valid']& (choice!=bdata.labels['choice']['none']) choiceRight = choice==bdata.labels['choice']['right'] possibleFreq = np.unique(targetFrequency) nFreq = len(possibleFreq) trialsEachFreq = behavioranalysis.find_trials_each_type(targetFrequency,possibleFreq)
subjects = ['adap011','adap012','adap013','adap014','adap015'] elif CASE==6: subjects = ['adap016','adap017','adap018','adap019','adap020'] elif CASE==7: subjects = ['adap021','adap022','adap023','adap024','adap025'] elif CASE==8: subjects = ['d1pi008','d1pi009','d1pi010','d1pi011','d1pi012'] elif CASE==0: subjects = ['adap010'] figure(CASE) # subjects = ['test011','test015','test016','test017', 'test012','test013','test014','test018','test019','test020'] # subjects = ['test011','test015','test016','test017','test018'] # subjects = ['test050','test052','test053', # 'test055','test056','test057','test058','test059'] #sessions = '20150311a' try: behavioranalysis.behavior_summary(subjects,session,trialslim=[0,1000],outputDir='/var/tmp/behavior_reports/') except: print 'Something is wrong with this session' raise pass ''' subjects = ['test011','test015','test016'] sessions = ['20150222a','20150223a'] behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/tmp/') '''
else: session = '20150308a' for CASE in [1]: if CASE==1: subjects = ['cued001','cued002','cued003','cued004','cued005','cued006'] elif CASE==2: pass figure(CASE) #behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/var/tmp/behavior_reports/') for inda,animalName in enumerate(subjects): fname=loadbehavior.path_to_behavior_data(animalName,'santiago','2afc',session) try: bdata=loadbehavior.BehaviorData(fname) nReward = bdata['nRewarded'][-1] nValid = bdata['nValid'][-1] correct = nReward/float(nValid) print '{0} (rew/valid): {1} / {2} = {3:0.0%}'.format(animalName,nReward,nValid,correct) except: print 'Something is wrong with this session' pass ''' subjects = ['test011','test015','test016'] sessions = ['20150222a','20150223a'] behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/tmp/') '''
def behav_sum(self): behavioranalysis.behavior_summary(self.subjects, self.sessions, outputDir=self.outputDir, paradigm=self.paradigm)
''' For Daily Behavior Monitoring. Loads behavior data from mounted jarahub/data/behavior for animals of interest, plot psychometric curve and dynamics data. ''' import sys # from jaratoolbox.test.nick import behavioranalysis_vnick as behavioranalysis from jaratoolbox import behavioranalysis reload(behavioranalysis) # subjects = ['amod001', 'amod002', 'amod003', 'amod004', 'amod005'] # subjects = ['adap026', 'adap027', 'adap028', 'adap029', 'adap030', ] # subjects = ['adap021', 'adap022', 'adap023', 'adap024', 'adap025' ] # subjects = ['adap022', 'adap026', 'adap027', 'adap030'] #New muscimol animals subjects = ['adap025', 'adap028', 'adap029'] if len(sys.argv)>1: sessions = sys.argv[1:] #sessions = input("Enter sessions (in a list of strings ['','']) to check behavior performance:") behavioranalysis.behavior_summary(subjects,sessions,trialslim=[0,1000],outputDir='/home/nick/data/behavior_reports')