def runTest(self):
choice = {0: 1, 1: -1, 2: 1}
RT = {0: 100, 1: 200, 2: 300}
valueLeft = {0: 0, 1: 1, 2: 2}
valueRight = {0: 3, 1: 2, 2: 1}
fixItem = {0: [2, 1], 1: [1, 2], 2: [1, 2]}
fixTime = {0: [50, 50], 1: [150, 50], 2: [150, 150]}
fixRDV = {0: [0.1, 0.2], 1: [0.5, 0.8], 2: [0.3, 0.6]}
numTrials = 3
util.save_simulations_to_csv(
choice, RT, valueLeft, valueRight, fixItem, fixTime, fixRDV,
numTrials)
choiceFile = open('choice.csv', 'r')
RTFile = open('rt.csv', 'r')
valueLeftFile = open('value_left.csv', 'r')
valueRightFile = open('value_right.csv', 'r')
fixItemFile = open('fix_item.csv', 'r')
fixTimeFile = open('fix_time.csv', 'r')
fixRDVFile = open('fix_rdv.csv', 'r')
self.assertEqual("0,1,-1,1\n", choiceFile.read())
self.assertEqual("0,100,200,300\n", RTFile.read())
self.assertEqual("0,0,1,2\n", valueLeftFile.read())
self.assertEqual("0,3,2,1\n", valueRightFile.read())
self.assertEqual("0,2,1,1\n1,1,2,2\n", fixItemFile.read())
self.assertEqual("0,50,150,150\n1,50,50,150\n", fixTimeFile.read())
self.assertEqual("0,0.1,0.5,0.3\n1,0.2,0.8,0.6\n", fixRDVFile.read())
os.remove('choice.csv')
os.remove('rt.csv')
os.remove('value_left.csv')
os.remove('value_right.csv')
os.remove('fix_item.csv')
os.remove('fix_time.csv')
os.remove('fix_rdv.csv')
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--num-threads", type=int, default=9,
help="Size of the thread pool.")
parser.add_argument("--trials-per-subject", type=int, default=100,
help="Number of trials from each subject to be used in "
"the analysis; if smaller than 1, all trials are used.")
parser.add_argument("--num-simulations", type=int, default=400,
help="Number of simulations to be generated per trial "
"condition.")
parser.add_argument("--range-d", nargs="+", type=float,
default=[0.003, 0.006, 0.009],
help="Search range for parameter d.")
parser.add_argument("--range-sigma", nargs="+", type=float,
default=[0.03, 0.06, 0.09],
help="Search range for parameter sigma.")
parser.add_argument("--range-theta", nargs="+", type=float,
default=[0.3, 0.5, 0.7],
help="Search range for parameter theta.")
parser.add_argument("--expdata-file-name", type=str, default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name", type=str,
default="fixations.csv", help="Name of fixations file.")
parser.add_argument("--use-cis-trials", default=False, action="store_true",
help="Use CIS trials in the analysis.")
parser.add_argument("--use-trans-trials", default=False,
action="store_true", help="Use TRANS trials in the "
"analysis.")
parser.add_argument("--save-simulations", default=False,
action="store_true", help="Save simulations to CSV.")
parser.add_argument("--verbose", default=False, action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
pool = Pool(args.num_threads)
# Load experimental data from CSV file.
try:
data = load_data_from_csv(
args.expdata_file_name, args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
choice = data.choice
valueLeft = data.valueLeft
valueRight = data.valueRight
fixItem = data.fixItem
fixTime = data.fixTime
isCisTrial = data.isCisTrial
isTransTrial = data.isTransTrial
# Maximum likelihood estimation.
# Grid search on the parameters of the model using odd trials only.
if args.verbose:
print("Starting grid search...")
models = list()
listParams = list()
for d in args.range_d:
for theta in args.range_theta:
for sigma in args.range_sigma:
models.append((d, theta, sigma))
params = (choice, valueLeft, valueRight, fixItem, fixTime, d,
theta, sigma, args.trials_per_subject, True, False,
isCisTrial, isTransTrial, args.use_cis_trials,
args.use_trans_trials, args.verbose)
listParams.append(params)
results = pool.map(get_model_nll_wrapper, listParams)
# Get optimal parameters.
minNegLogLikeIdx = results.index(min(results))
optimD = models[minNegLogLikeIdx][0]
optimTheta = models[minNegLogLikeIdx][1]
optimSigma = models[minNegLogLikeIdx][2]
if args.verbose:
print("Finished grid search!")
print("Optimal d: " + str(optimD))
print("Optimal theta: " + str(optimTheta))
print("Optimal sigma: " + str(optimSigma))
print("Min NLL: " + str(min(results)))
# Get empirical distributions from even trials only.
try:
dists = get_empirical_distributions(
valueLeft, valueRight, fixItem, fixTime, useOddTrials=False,
useEvenTrials=True, isCisTrial=isCisTrial,
isTransTrial=isTransTrial, useCisTrials=args.use_cis_trials,
useTransTrials=args.use_trans_trials)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Parameters for generating simulations.
orientations = range(-15,20,5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
if oLeft != oRight and args.use_cis_trials and oLeft * oRight >= 0:
trialConditions.append((vLeft, vRight))
elif (oLeft != oRight and args.use_trans_trials and
oLeft * oRight <= 0):
trialConditions.append((vLeft, vRight))
# Generate simulations using the empirical distributions and the
# estimated parameters.
try:
simul = run_simulations(
probLeftFixFirst, distLatencies, distTransitions, distFixations,
args.num_simulations, trialConditions, optimD, optimTheta,
sigma=optimSigma)
except Exception as e:
print("An exception occurred while running simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
if args.save_simulations:
totalTrials = args.num_simulations * len(trialConditions)
save_simulations_to_csv(
simulChoice, simulRT, simulValueLeft, simulValueRight, simulFixItem,
simulFixTime, simulFixRDV, totalTrials)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("subject", type=str, help="Subject name.")
parser.add_argument("--num-threads", type=int, default=9,
help="Size of the thread pool.")
parser.add_argument("--num-trials", type=int, default=100,
help="Number of trials to be used in the analysis; if "
"smaller than 1, all trials are used.")
parser.add_argument("--num-samples", type=int, default=32,
help="Number of samples to be drawn from the posterior "
"distribution when generating simulations.")
parser.add_argument("--num-simulations-per-sample", type=int, default=1,
help="Number of simulations to be genearated for each "
"sample drawn from the posterior distribution.")
parser.add_argument("--range-d", nargs="+", type=float,
default=[0.003, 0.006, 0.009],
help="Search range for parameter d.")
parser.add_argument("--range-sigma", nargs="+", type=float,
default=[0.03, 0.06, 0.09],
help="Search range for parameter sigma.")
parser.add_argument("--range-theta", nargs="+", type=float,
default=[0.3, 0.5, 0.7],
help="Search range for parameter theta.")
parser.add_argument("--expdata-file-name", type=str, default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name", type=str,
default="fixations.csv", help="Name of fixations file.")
parser.add_argument("--save-simulations", default=False,
action="store_true", help="Save simulations to CSV.")
parser.add_argument("--verbose", default=False, action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
pool = Pool(args.num_threads)
choice = dict()
valueLeft = dict()
valueRight = dict()
fixItem = dict()
fixTime = dict()
# Load experimental data from CSV file.
try:
data = load_data_from_csv(
args.expdata_file_name, args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
choice[args.subject] = data.choice[args.subject]
valueLeft[args.subject] = data.valueLeft[args.subject]
valueRight[args.subject] = data.valueRight[args.subject]
fixItem[args.subject] = data.fixItem[args.subject]
fixTime[args.subject] = data.fixTime[args.subject]
# Posteriors estimation for the parameters of the model, using odd trials.
if args.verbose:
print("Starting grid search for subject " + args.subject + "...")
numModels = (len(args.range_d) * len(args.range_theta) *
len(args.range_sigma))
models = list()
posteriors = dict()
for d in args.range_d:
for theta in args.range_theta:
for sigma in args.range_sigma:
model = (d, theta, sigma)
models.append(model)
posteriors[model] = 1. / numModels
subjects = choice.keys()
for subject in subjects:
trials = choice[subject].keys()
if args.num_trials < 1:
args.num_trials = len(trials)
trialSet = np.random.choice(
[trial for trial in trials if trial % 2],
args.num_trials, replace=False)
for trial in trialSet:
if not trial % 2:
continue
listParams = list()
for model in models:
listParams.append(
(choice[subject][trial], valueLeft[subject][trial],
valueRight[subject][trial], fixItem[subject][trial],
fixTime[subject][trial], model[0], model[1], model[2]))
try:
likelihoods = pool.map(get_trial_likelihood_wrapper, listParams)
except Exception as e:
print("An exception occurred during the likelihood computation "
"for trial " + str(trial) + ": " + str(e))
return
# Get the denominator for normalizing the posteriors.
i = 0
denominator = 0
for model in models:
denominator += posteriors[model] * likelihoods[i]
i += 1
if denominator == 0:
continue
# Calculate the posteriors after this trial.
i = 0
for model in models:
prior = posteriors[model]
posteriors[model] = likelihoods[i] * prior / denominator
i += 1
if args.verbose:
for model in posteriors:
print("P" + str(model) + " = " + str(posteriors[model]))
print("Sum: " + str(sum(posteriors.values())))
if args.verbose:
print("Finished grid search!")
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(
valueLeft, valueRight, fixItem, fixTime, useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15,20,5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Generate probabilistic simulations using the posteriors distribution.
try:
simul = generate_probabilistic_simulations(
probLeftFixFirst, distLatencies, distTransitions, distFixations,
trialConditions, posteriors, args.num_samples,
args.num_simulations_per_sample)
except Exception as e:
print("An exception occurred while running simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
if args.save_simulations:
totalTrials = len(simulRT.keys())
save_simulations_to_csv(
simulChoice, simulRT, simulValueLeft, simulValueRight, simulFixItem,
simulFixTime, simulFixRDV, totalTrials)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--num-threads",
type=int,
default=9,
help="Size of the thread pool.")
parser.add_argument(
"--trials-per-subject",
type=int,
default=100,
help="Number of trials from each subject to be used in "
"the analysis; if smaller than 1, all trials are used.")
parser.add_argument(
"--num-samples",
type=int,
default=100,
help="Number of samples to be drawn from the posterior "
"distribution when generating simulations.")
parser.add_argument("--num-simulations-per-sample",
type=int,
default=10,
help="Number of simulations to be genearated for each "
"sample drawn from the posterior distribution.")
parser.add_argument("--range-d",
nargs="+",
type=float,
default=[0.003, 0.006, 0.009],
help="Search range for parameter d.")
parser.add_argument("--range-sigma",
nargs="+",
type=float,
default=[0.03, 0.06, 0.09],
help="Search range for parameter sigma.")
parser.add_argument("--range-theta",
nargs="+",
type=float,
default=[0.3, 0.5, 0.7],
help="Search range for parameter theta.")
parser.add_argument("--expdata-file-name",
type=str,
default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name",
type=str,
default="fixations.csv",
help="Name of fixations file.")
parser.add_argument("--save-simulations",
default=False,
action="store_true",
help="Save simulations to CSV.")
parser.add_argument("--verbose",
default=False,
action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
pool = Pool(args.num_threads)
# Load experimental data from CSV file.
try:
data = load_data_from_csv(args.expdata_file_name,
args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
choice = data.choice
valueLeft = data.valueLeft
valueRight = data.valueRight
fixItem = data.fixItem
fixTime = data.fixTime
# Posteriors estimation for the parameters of the model, using odd trials.
if args.verbose:
print("Starting grid search...")
numModels = (len(args.range_d) * len(args.range_theta) *
len(args.range_sigma))
models = list()
posteriors = dict()
for d in args.range_d:
for theta in args.range_theta:
for sigma in args.range_sigma:
model = (d, theta, sigma)
models.append(model)
posteriors[model] = 1. / numModels
subjects = choice.keys()
for subject in subjects:
if args.verbose:
print("Running subject " + subject + "...")
trials = choice[subject].keys()
if args.trials_per_subject < 1:
args.trials_per_subject = len(trials)
trialSet = np.random.choice([trial for trial in trials if trial % 2],
args.trials_per_subject,
replace=False)
for trial in trialSet:
listParams = list()
for model in models:
listParams.append(
(choice[subject][trial], valueLeft[subject][trial],
valueRight[subject][trial], fixItem[subject][trial],
fixTime[subject][trial], model[0], model[1], model[2]))
try:
likelihoods = pool.map(get_trial_likelihood_wrapper,
listParams)
except Exception as e:
print(
"An exception occurred during the likelihood computation "
"for subject " + subject + ", trial " + str(trial) + ": " +
str(e))
return
# Get the denominator for normalizing the posteriors.
i = 0
denominator = 0
for model in models:
denominator += posteriors[model] * likelihoods[i]
i += 1
if denominator == 0:
continue
# Calculate the posteriors after this trial.
i = 0
for model in models:
prior = posteriors[model]
posteriors[model] = likelihoods[i] * prior / denominator
i += 1
if args.verbose:
for model in posteriors:
print("P" + str(model) + " = " + str(posteriors[model]))
print("Sum: " + str(sum(posteriors.values())))
if args.verbose:
print("Finished grid search!")
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(valueLeft,
valueRight,
fixItem,
fixTime,
useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15, 20, 5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Generate probabilistic simulations using the posteriors distribution.
try:
simul = generate_probabilistic_simulations(
probLeftFixFirst, distLatencies, distTransitions, distFixations,
trialConditions, posteriors, args.num_samples,
args.num_simulations_per_sample)
except Exception as e:
print("An exception occurred while running simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
if args.save_simulations:
totalTrials = len(simulRT.keys())
save_simulations_to_csv(simulChoice, simulRT, simulValueLeft,
simulValueRight, simulFixItem, simulFixTime,
simulFixRDV, totalTrials)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("subject", type=str, help="Subject name")
parser.add_argument("--num-threads", type=int, default=9,
help="Size of the thread pool.")
parser.add_argument("--num-trials", type=int, default=100,
help="Number of trials to be used in the analysis; if "
"smaller than 1, all trials are used.")
parser.add_argument("--num-simulations", type=int, default=32,
help="Number of simulations to be generated per trial "
"condition.")
parser.add_argument("--range-d", nargs="+", type=float,
default=[0.003, 0.006, 0.009],
help="Search range for parameter d.")
parser.add_argument("--range-sigma", nargs="+", type=float,
default=[0.03, 0.06, 0.09],
help="Search range for parameter sigma.")
parser.add_argument("--range-theta", nargs="+", type=float,
default=[0.3, 0.5, 0.7],
help="Search range for parameter theta.")
parser.add_argument("--expdata-file-name", type=str, default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name", type=str,
default="fixations.csv", help="Name of fixations file.")
parser.add_argument("--save-simulations", default=False,
action="store_true", help="Save simulations to CSV.")
parser.add_argument("--save-figures", default=False,
action="store_true", help="Save figures comparing "
"choice and RT curves for data and simulations.")
parser.add_argument("--verbose", default=False, action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
pool = Pool(args.num_threads)
choice = dict()
valueLeft = dict()
valueRight = dict()
fixItem = dict()
fixTime = dict()
# Load experimental data from CSV file.
try:
data = load_data_from_csv(
args.expdata_file_name, args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
choice[args.subject] = data.choice[args.subject]
valueLeft[args.subject] = data.valueLeft[args.subject]
valueRight[args.subject] = data.valueRight[args.subject]
fixItem[args.subject] = data.fixItem[args.subject]
fixTime[args.subject] = data.fixTime[args.subject]
# Maximum likelihood estimation using odd trials only.
# Grid search on the parameters of the model.
if args.verbose:
print("Starting grid search for subject " + args.subject + "...")
models = list()
listParams = list()
for d in args.range_d:
for theta in args.range_theta:
for sigma in args.range_sigma:
models.append((d, theta, sigma))
params = (choice, valueLeft, valueRight, fixItem, fixTime, d,
theta, sigma, args.num_trials, True, False,
args.verbose)
listParams.append(params)
results = pool.map(get_model_nll_wrapper, listParams)
# Get optimal parameters.
minNegLogLikeIdx = results.index(min(results))
optimD = models[minNegLogLikeIdx][0]
optimTheta = models[minNegLogLikeIdx][1]
optimSigma = models[minNegLogLikeIdx][2]
if args.verbose:
print("Finished grid search!")
print("Optimal d: " + str(optimD))
print("Optimal theta: " + str(optimTheta))
print("Optimal sigma: " + str(optimSigma))
print("Min NLL: " + str(min(results)))
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(
valueLeft, valueRight, fixItem, fixTime, useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15,20,5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Generate simulations using the even trials distributions and the
# estimated parameters.
try:
simul = run_simulations(
probLeftFixFirst, distLatencies, distTransitions, distFixations,
args.num_simulations, trialConditions, optimD, optimTheta,
sigma=optimSigma)
except Exception as e:
print("An exception occurred while running simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
totalTrials = args.num_simulations * len(trialConditions)
if args.save_simulations:
save_simulations_to_csv(
simulChoice, simulRT, simulValueLeft, simulValueRight, simulFixItem,
simulFixTime, simulFixRDV, totalTrials)
if args.save_figures:
# Create pdf file to save figures.
pp = PdfPages(
"figures_" + str(optimD) + "_" + str(optimTheta) + "_" +
str(optimSigma) + "_" + str(args.num_simulations) + ".pdf")
# Generate choice and RT curves for real data (odd trials) and
# simulations (generated from even trials).
fig1 = generate_choice_curves(
choice, valueLeft, valueRight, simulChoice, simulValueLeft,
simulValueRight, totalTrials)
pp.savefig(fig1)
fig2 = generate_rt_curves(
RT, valueLeft, valueRight, simulRT, simulValueLeft, simulValueRight,
totalTrials)
pp.savefig(fig2)
pp.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("subject", type=str, help="Subject name")
parser.add_argument("--num-threads",
type=int,
default=9,
help="Size of the thread pool.")
parser.add_argument("--num-trials",
type=int,
default=100,
help="Number of trials to be used in the analysis; if "
"smaller than 1, all trials are used.")
parser.add_argument("--num-simulations",
type=int,
default=32,
help="Number of simulations to be generated per trial "
"condition.")
parser.add_argument("--range-d",
nargs="+",
type=float,
default=[0.003, 0.006, 0.009],
help="Search range for parameter d.")
parser.add_argument("--range-sigma",
nargs="+",
type=float,
default=[0.03, 0.06, 0.09],
help="Search range for parameter sigma.")
parser.add_argument("--range-theta",
nargs="+",
type=float,
default=[0.3, 0.5, 0.7],
help="Search range for parameter theta.")
parser.add_argument("--expdata-file-name",
type=str,
default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name",
type=str,
default="fixations.csv",
help="Name of fixations file.")
parser.add_argument("--save-simulations",
default=False,
action="store_true",
help="Save simulations to CSV.")
parser.add_argument("--save-figures",
default=False,
action="store_true",
help="Save figures comparing "
"choice and RT curves for data and simulations.")
parser.add_argument("--verbose",
default=False,
action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
pool = Pool(args.num_threads)
choice = dict()
valueLeft = dict()
valueRight = dict()
fixItem = dict()
fixTime = dict()
# Load experimental data from CSV file.
try:
data = load_data_from_csv(args.expdata_file_name,
args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
choice[args.subject] = data.choice[args.subject]
valueLeft[args.subject] = data.valueLeft[args.subject]
valueRight[args.subject] = data.valueRight[args.subject]
fixItem[args.subject] = data.fixItem[args.subject]
fixTime[args.subject] = data.fixTime[args.subject]
# Maximum likelihood estimation using odd trials only.
# Grid search on the parameters of the model.
if args.verbose:
print("Starting grid search for subject " + args.subject + "...")
models = list()
listParams = list()
for d in args.range_d:
for theta in args.range_theta:
for sigma in args.range_sigma:
models.append((d, theta, sigma))
params = (choice, valueLeft, valueRight, fixItem, fixTime, d,
theta, sigma, args.num_trials, True, False,
args.verbose)
listParams.append(params)
results = pool.map(get_model_nll_wrapper, listParams)
# Get optimal parameters.
minNegLogLikeIdx = results.index(min(results))
optimD = models[minNegLogLikeIdx][0]
optimTheta = models[minNegLogLikeIdx][1]
optimSigma = models[minNegLogLikeIdx][2]
if args.verbose:
print("Finished grid search!")
print("Optimal d: " + str(optimD))
print("Optimal theta: " + str(optimTheta))
print("Optimal sigma: " + str(optimSigma))
print("Min NLL: " + str(min(results)))
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(valueLeft,
valueRight,
fixItem,
fixTime,
useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15, 20, 5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Generate simulations using the even trials distributions and the
# estimated parameters.
try:
simul = run_simulations(probLeftFixFirst,
distLatencies,
distTransitions,
distFixations,
args.num_simulations,
trialConditions,
optimD,
optimTheta,
sigma=optimSigma)
except Exception as e:
print("An exception occurred while running simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
totalTrials = args.num_simulations * len(trialConditions)
if args.save_simulations:
save_simulations_to_csv(simulChoice, simulRT, simulValueLeft,
simulValueRight, simulFixItem, simulFixTime,
simulFixRDV, totalTrials)
if args.save_figures:
# Create pdf file to save figures.
pp = PdfPages("figures_" + str(optimD) + "_" + str(optimTheta) + "_" +
str(optimSigma) + "_" + str(args.num_simulations) +
".pdf")
# Generate choice and RT curves for real data (odd trials) and
# simulations (generated from even trials).
fig1 = generate_choice_curves(choice, valueLeft, valueRight,
simulChoice, simulValueLeft,
simulValueRight, totalTrials)
pp.savefig(fig1)
fig2 = generate_rt_curves(RT, valueLeft, valueRight, simulRT,
simulValueLeft, simulValueRight, totalTrials)
pp.savefig(fig2)
pp.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--bin-step", type=int, default=10,
help="Size of the bin step to be used in the fixation "
"distributions.")
parser.add_argument("--max-fix-bin", type=int, default=3000,
help="Maximum fixation length to be used in the "
"fixation distributions.")
parser.add_argument("--num-fix-dists", type=int, default=3,
help="Number of fixation distributions.")
parser.add_argument("--num-iterations", type=int, default=3,
help="Number of iterations used to approximate the"
"true distributions.")
parser.add_argument("--num-simulations", type=int, default=400,
help="Number of simulations to be generated per trial "
"condition.")
parser.add_argument("--d", type=float, default=0.004,
help="aDDM parameter for generating simulations.")
parser.add_argument("--sigma", type=float, default=0.07,
help="aDDM parameter for generating simulations.")
parser.add_argument("--theta", type=float, default=0.25,
help="aDDM parameter for generating simulations.")
parser.add_argument("--expdata-file-name", type=str, default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name", type=str,
default="fixations.csv", help="Name of fixations file.")
parser.add_argument("--save-simulations", default=False,
action="store_true", help="Save simulations to CSV.")
parser.add_argument("--verbose", default=False, action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
# Time bins to be used in the fixation distributions.
bins = range(args.bin_step, args.max_fix_bin + args.bin_step, args.bin_step)
# Load experimental data from CSV file.
try:
data = load_data_from_csv(
args.expdata_file_name, args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
RT = data.RT
choice = data.choice
valueLeft = data.valueLeft
valueRight = data.valueRight
fixItem = data.fixItem
fixTime = data.fixTime
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(
valueLeft, valueRight, fixItem, fixTime, useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15,20,5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Create original empirical distributions of fixations.
empiricalFixDist = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
empiricalFixDist[numFix] = dict()
for valueDiff in xrange(-3,4):
empiricalFixDist[numFix][valueDiff] = dict()
for bin in bins:
empiricalFixDist[numFix][valueDiff][bin] = 0
for fixTime in distFixations[numFix][valueDiff]:
bin = args.bin_step * min((fixTime // args.bin_step) + 1,
len(bins))
empiricalFixDist[numFix][valueDiff][bin] += 1
# Normalize the distributions.
for numFix in xrange(1, args.num_fix_dists + 1):
for valueDiff in xrange(-3,4):
sumBins = sum(empiricalFixDist[numFix][valueDiff].values())
for bin in bins:
empiricalFixDist[numFix][valueDiff][bin] = (
float(empiricalFixDist[numFix][valueDiff][bin]) /
float(sumBins))
for it in xrange(args.num_iterations):
if args.verbose:
print("Iteration " + str(it + 1) + "/" + str(args.num_iterations))
# Generate simulations using the current empirical distributions and the
# model parameters.
try:
simul = run_simulations(
probLeftFixFirst, distLatencies, distTransitions,
empiricalFixDist, args.num_simulations, trialConditions, args.d,
args.theta, args.sigma, bins, args.num_fix_dists)
except Exception as e:
print("An exception occurred while running simulations in " +
"iteration " + str(it) + ": " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
simulUninterruptedLastFixTime = simul.uninterruptedLastFixTime
countLastFix = dict()
countTotal = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
countLastFix[numFix] = dict()
countTotal[numFix] = dict()
for valueDiff in xrange(-3,4):
countLastFix[numFix][valueDiff] = dict()
countTotal[numFix][valueDiff] = dict()
for bin in bins:
countLastFix[numFix][valueDiff][bin] = 0
countTotal[numFix][valueDiff][bin] = 0
for trial in simulRT.keys():
# Count all item fixations, except last.
fixUnfixValueDiffs = {
1: simulValueLeft[trial] - simulValueRight[trial],
2: simulValueRight[trial] - simulValueLeft[trial]}
lastItemFixSkipped = False
lastFixItem = -1
numFix = 1
for item, time in zip(
simulFixItem[trial][::-1], simulFixTime[trial][::-1]):
if not lastItemFixSkipped and (item == 1 or item == 2):
lastFixItem = item
lastItemFixSkipped = True
continue
if item == 1 or item == 2:
bin = args.bin_step * min((time // args.bin_step) + 1,
len(bins))
vDiff = fixUnfixValueDiffs[item]
countTotal[numFix][vDiff][bin] += 1
if numFix < args.num_fix_dists:
numFix += 1
# Count last fixation.
vDiff = fixUnfixValueDiffs[lastFixItem]
bin = args.bin_step * min(
(simulUninterruptedLastFixTime[trial] // args.bin_step) + 1,
len(bins))
countLastFix[numFix][vDiff][bin] += 1
countTotal[numFix][vDiff][bin] += 1
# Obtain true distributions of fixations.
trueFixDist = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
trueFixDist[numFix] = dict()
for valueDiff in xrange(-3,4):
trueFixDist[numFix][valueDiff] = dict()
for bin in bins:
probNotLastFix = 1
if countTotal[numFix][valueDiff][bin] > 0:
probNotLastFix = 1 - (
float(countLastFix[numFix][valueDiff][bin]) /
float(countTotal[numFix][valueDiff][bin]))
if probNotLastFix == 0:
trueFixDist[numFix][valueDiff][bin] = (
empiricalFixDist[numFix][valueDiff][bin])
else:
trueFixDist[numFix][valueDiff][bin] = (
float(empiricalFixDist[numFix][valueDiff][bin]) /
float(probNotLastFix))
# Normalize the distributions.
for numFix in xrange(1, args.num_fix_dists + 1):
for valueDiff in xrange(-3,4):
sumBins = sum(trueFixDist[numFix][valueDiff].values())
if sumBins > 0:
for bin in bins:
trueFixDist[numFix][valueDiff][bin] = (
float(trueFixDist[numFix][valueDiff][bin]) /
float(sumBins))
# Update empirical distributions using the current true distributions.
empiricalFixDist = trueFixDist
# Generate final simulations.
try:
simul = run_simulations(
probLeftFixFirst, distLatencies, distTransitions, empiricalFixDist,
args.num_simulations, trialConditions, args.d, args.theta,
args.sigma, bins, args.num_fix_dists)
except Exception as e:
print("An exception occurred while running the final " +
"simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
simulUninterruptedLastFixTime = simul.uninterruptedLastFixTime
if args.save_simulations:
totalTrials = args.num_simulations * len(trialConditions)
save_simulations_to_csv(
simulChoice, simulRT, simulValueLeft, simulValueRight, simulFixItem,
simulFixTime, simulFixRDV, totalTrials)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--bin-step",
type=int,
default=10,
help="Size of the bin step to be used in the fixation "
"distributions.")
parser.add_argument("--max-fix-bin",
type=int,
default=3000,
help="Maximum fixation length to be used in the "
"fixation distributions.")
parser.add_argument("--num-fix-dists",
type=int,
default=3,
help="Number of fixation distributions.")
parser.add_argument("--num-iterations",
type=int,
default=3,
help="Number of iterations used to approximate the"
"true distributions.")
parser.add_argument("--num-simulations",
type=int,
default=400,
help="Number of simulations to be generated per trial "
"condition.")
parser.add_argument("--d",
type=float,
default=0.004,
help="aDDM parameter for generating simulations.")
parser.add_argument("--sigma",
type=float,
default=0.07,
help="aDDM parameter for generating simulations.")
parser.add_argument("--theta",
type=float,
default=0.25,
help="aDDM parameter for generating simulations.")
parser.add_argument("--expdata-file-name",
type=str,
default="expdata.csv",
help="Name of experimental data file.")
parser.add_argument("--fixations-file-name",
type=str,
default="fixations.csv",
help="Name of fixations file.")
parser.add_argument("--save-simulations",
default=False,
action="store_true",
help="Save simulations to CSV.")
parser.add_argument("--verbose",
default=False,
action="store_true",
help="Increase output verbosity.")
args = parser.parse_args()
# Time bins to be used in the fixation distributions.
bins = range(args.bin_step, args.max_fix_bin + args.bin_step,
args.bin_step)
# Load experimental data from CSV file.
try:
data = load_data_from_csv(args.expdata_file_name,
args.fixations_file_name,
useAngularDists=True)
except Exception as e:
print("An exception occurred while loading the data: " + str(e))
return
RT = data.RT
choice = data.choice
valueLeft = data.valueLeft
valueRight = data.valueRight
fixItem = data.fixItem
fixTime = data.fixTime
# Get empirical distributions from even trials.
try:
dists = get_empirical_distributions(valueLeft,
valueRight,
fixItem,
fixTime,
useOddTrials=False,
useEvenTrials=True)
except Exception as e:
print("An exception occurred while getting empirical distributions: " +
str(e))
return
probLeftFixFirst = dists.probLeftFixFirst
distLatencies = dists.distLatencies
distTransitions = dists.distTransitions
distFixations = dists.distFixations
# Trial conditions for generating simulations.
orientations = range(-15, 20, 5)
trialConditions = list()
for oLeft in orientations:
for oRight in orientations:
if oLeft != oRight:
vLeft = np.absolute((np.absolute(oLeft) - 15) / 5)
vRight = np.absolute((np.absolute(oRight) - 15) / 5)
trialConditions.append((vLeft, vRight))
# Create original empirical distributions of fixations.
empiricalFixDist = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
empiricalFixDist[numFix] = dict()
for valueDiff in xrange(-3, 4):
empiricalFixDist[numFix][valueDiff] = dict()
for bin in bins:
empiricalFixDist[numFix][valueDiff][bin] = 0
for fixTime in distFixations[numFix][valueDiff]:
bin = args.bin_step * min(
(fixTime // args.bin_step) + 1, len(bins))
empiricalFixDist[numFix][valueDiff][bin] += 1
# Normalize the distributions.
for numFix in xrange(1, args.num_fix_dists + 1):
for valueDiff in xrange(-3, 4):
sumBins = sum(empiricalFixDist[numFix][valueDiff].values())
for bin in bins:
empiricalFixDist[numFix][valueDiff][bin] = (
float(empiricalFixDist[numFix][valueDiff][bin]) /
float(sumBins))
for it in xrange(args.num_iterations):
if args.verbose:
print("Iteration " + str(it + 1) + "/" + str(args.num_iterations))
# Generate simulations using the current empirical distributions and the
# model parameters.
try:
simul = run_simulations(probLeftFixFirst, distLatencies,
distTransitions, empiricalFixDist,
args.num_simulations, trialConditions,
args.d, args.theta, args.sigma, bins,
args.num_fix_dists)
except Exception as e:
print("An exception occurred while running simulations in " +
"iteration " + str(it) + ": " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
simulUninterruptedLastFixTime = simul.uninterruptedLastFixTime
countLastFix = dict()
countTotal = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
countLastFix[numFix] = dict()
countTotal[numFix] = dict()
for valueDiff in xrange(-3, 4):
countLastFix[numFix][valueDiff] = dict()
countTotal[numFix][valueDiff] = dict()
for bin in bins:
countLastFix[numFix][valueDiff][bin] = 0
countTotal[numFix][valueDiff][bin] = 0
for trial in simulRT.keys():
# Count all item fixations, except last.
fixUnfixValueDiffs = {
1: simulValueLeft[trial] - simulValueRight[trial],
2: simulValueRight[trial] - simulValueLeft[trial]
}
lastItemFixSkipped = False
lastFixItem = -1
numFix = 1
for item, time in zip(simulFixItem[trial][::-1],
simulFixTime[trial][::-1]):
if not lastItemFixSkipped and (item == 1 or item == 2):
lastFixItem = item
lastItemFixSkipped = True
continue
if item == 1 or item == 2:
bin = args.bin_step * min(
(time // args.bin_step) + 1, len(bins))
vDiff = fixUnfixValueDiffs[item]
countTotal[numFix][vDiff][bin] += 1
if numFix < args.num_fix_dists:
numFix += 1
# Count last fixation.
vDiff = fixUnfixValueDiffs[lastFixItem]
bin = args.bin_step * min(
(simulUninterruptedLastFixTime[trial] // args.bin_step) + 1,
len(bins))
countLastFix[numFix][vDiff][bin] += 1
countTotal[numFix][vDiff][bin] += 1
# Obtain true distributions of fixations.
trueFixDist = dict()
for numFix in xrange(1, args.num_fix_dists + 1):
trueFixDist[numFix] = dict()
for valueDiff in xrange(-3, 4):
trueFixDist[numFix][valueDiff] = dict()
for bin in bins:
probNotLastFix = 1
if countTotal[numFix][valueDiff][bin] > 0:
probNotLastFix = 1 - (
float(countLastFix[numFix][valueDiff][bin]) /
float(countTotal[numFix][valueDiff][bin]))
if probNotLastFix == 0:
trueFixDist[numFix][valueDiff][bin] = (
empiricalFixDist[numFix][valueDiff][bin])
else:
trueFixDist[numFix][valueDiff][bin] = (
float(empiricalFixDist[numFix][valueDiff][bin]) /
float(probNotLastFix))
# Normalize the distributions.
for numFix in xrange(1, args.num_fix_dists + 1):
for valueDiff in xrange(-3, 4):
sumBins = sum(trueFixDist[numFix][valueDiff].values())
if sumBins > 0:
for bin in bins:
trueFixDist[numFix][valueDiff][bin] = (
float(trueFixDist[numFix][valueDiff][bin]) /
float(sumBins))
# Update empirical distributions using the current true distributions.
empiricalFixDist = trueFixDist
# Generate final simulations.
try:
simul = run_simulations(probLeftFixFirst, distLatencies,
distTransitions, empiricalFixDist,
args.num_simulations, trialConditions, args.d,
args.theta, args.sigma, bins,
args.num_fix_dists)
except Exception as e:
print("An exception occurred while running the final " +
"simulations: " + str(e))
return
simulRT = simul.RT
simulChoice = simul.choice
simulValueLeft = simul.valueLeft
simulValueRight = simul.valueRight
simulFixItem = simul.fixItem
simulFixTime = simul.fixTime
simulFixRDV = simul.fixRDV
simulUninterruptedLastFixTime = simul.uninterruptedLastFixTime
if args.save_simulations:
totalTrials = args.num_simulations * len(trialConditions)
save_simulations_to_csv(simulChoice, simulRT, simulValueLeft,
simulValueRight, simulFixItem, simulFixTime,
simulFixRDV, totalTrials)