def SR_reg(data):
C = []
dm = data['DM'][0]
firing = data['Data'][0]
for s, sess in enumerate(dm):
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:,1]
reward = DM[:,2]
ones = np.ones(len(reward))
predictors_all = OrderedDict([('Reward', reward),
('Choice', choices),
('ones', ones)])
X = np.vstack(predictors_all.values()).T[:len(choices),:].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape([len(firing_rates),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors,n_neurons,n_timepoints)) # Predictor loadings
C = np.concatenate(C,1)
return C
def time_in_block(data, area='PFC'):
dm = data['DM'][0]
firing = data['Data'][0]
C_1 = []
C_2 = []
C_3 = []
cpd_1 = []
cpd_2 = []
cpd_3 = []
# cpd_perm_p_1 = []; cpd_perm_p_2 = []; cpd_perm_p_3 = []
for s, sess in enumerate(dm):
DM = dm[s]
firing_rates = firing[s][1:]
# firing_rates = firing_rates[:,:,:63]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1] - 0.5
reward = DM[:, 2] - 0.5
task = DM[:, 5][1:]
a_pokes = DM[:, 6][1:]
b_pokes = DM[:, 7][1:]
reward_prev = reward[:-1]
reward = reward[1:]
choices_prev = choices[:-1]
choices = choices[1:]
taskid = task_ind(task, a_pokes, b_pokes)
task_1 = np.where(taskid == 1)[0]
task_2 = np.where(taskid == 2)[0]
task_3 = np.where(taskid == 3)[0]
reward_PE = np.zeros(len(task))
for r, rr in enumerate(reward):
if reward[r] != reward[r - 1]:
reward_PE[r] = 0.5
elif reward[r] == reward[r - 1]:
reward_PE[r] = -0.5
choice_PE = np.zeros(len(task))
for r, rr in enumerate(choices):
if choices[r] != choices[r - 1]:
choice_PE[r] = 0.5
elif choices[r] == choices[r - 1]:
choice_PE[r] = -0.5
reward_PE_1 = reward_PE[task_1]
choice_PE_1 = choice_PE[task_1]
rewards_1 = reward[task_1]
choices_1 = choices[task_1]
rewards_1 = reward[task_1]
ones_1 = np.ones(len(choices_1))
trials_1 = len(choices_1)
prev_reward_1 = reward_prev[task_1]
prev_choice_1 = choices_prev[task_1]
#prev_choice_1 = choices_1*choice_PE_1
choice_PE_1_reward_current = choice_PE_1 * rewards_1
choice_PE_1_reward_prev = choice_PE_1 * prev_reward_1
rew_ch_1 = choices_1 * rewards_1
prev_choice_1_lr = prev_choice_1 * prev_reward_1
firing_rates_1 = firing_rates[task_1]
predictors_all = OrderedDict([
('Choice', choices_1), ('Reward', rewards_1),
('Reward Repeat/Switch', reward_PE_1),
('Choice Repeat/Switch', choice_PE_1),
('Repeat/Switch Current Reward', choice_PE_1_reward_current),
('Repeat/Switch Prev Reward', choice_PE_1_reward_prev),
('Choice x Reward ', rew_ch_1),
('Prev Ch x Last Reward', prev_choice_1_lr),
('Prev Rew', prev_reward_1), ('Prev Ch', prev_choice_1),
('ones', ones_1)
])
X_1 = np.vstack(predictors_all.values()).T[:trials_1, :].astype(float)
n_predictors = X_1.shape[1]
y_1 = firing_rates_1.reshape(
[len(firing_rates_1),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_1, X_1)
C_1.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_1.append(
re._CPD(X_1, y_1).reshape(n_neurons, n_timepoints, n_predictors))
choices_2 = choices[task_2]
rewards_2 = reward[task_2]
ones_2 = np.ones(len(choices_2))
reward_PE_2 = reward_PE[task_2]
choice_PE_2 = choice_PE[task_2]
prev_reward_2 = reward_prev[task_2]
prev_choice_2 = choices_prev[task_2]
#prev_choice_2 = choices_2*choice_PE_2
choice_PE_2_reward_current = choice_PE_2 * rewards_2
choice_PE_2_reward_prev = choice_PE_2 * prev_reward_2
trials_2 = len(choices_2)
rew_ch_2 = choices_2 * rewards_2
prev_choice_2_lr = prev_choice_2 * prev_reward_2
ones_2 = np.ones(len(choices_2))
firing_rates_2 = firing_rates[task_2]
predictors_all = OrderedDict([
('Choice', choices_2), ('Reward', rewards_2),
('Reward Repeat/Switch', reward_PE_2),
('Choice Repeat/Switch', choice_PE_2),
('Repeat/Switch Current Reward', choice_PE_2_reward_current),
('Repeat/Switch Prev Reward', choice_PE_2_reward_prev),
('Choice x Reward ', rew_ch_2),
(' Prev Ch x Last Reward', prev_choice_2_lr),
('Prev Rew', prev_reward_2), ('Prev Ch', prev_choice_2),
('ones', ones_2)
])
X_2 = np.vstack(predictors_all.values()).T[:trials_2, :].astype(float)
n_predictors = X_2.shape[1]
y_2 = firing_rates_2.reshape(
[len(firing_rates_2),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_2, X_2)
C_2.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_2.append(
re._CPD(X_2, y_2).reshape(n_neurons, n_timepoints, n_predictors))
choices_3 = choices[task_3]
rewards_3 = reward[task_3]
ones_3 = np.ones(len(choices_3))
trials_3 = len(choices_3)
ones_3 = np.ones(len(choices_3))
prev_reward_3 = reward_prev[task_3]
choice_PE_3 = choice_PE[task_3]
reward_PE_3 = reward_PE[task_3]
choice_PE_3_reward_current = choice_PE_3 * rewards_3
choice_PE_3_reward_prev = choice_PE_3 * prev_reward_3
prev_choice_3 = choices_prev[task_3]
#prev_choice_3 = choices_3*choice_PE_3
rew_ch_3 = choices_3 * rewards_3
prev_choice_3_lr = prev_choice_3 * prev_reward_3
firing_rates_3 = firing_rates[task_3]
predictors_all = OrderedDict([
('Ch', choices_3), ('Rew', rewards_3), ('Rew Stay', reward_PE_3),
('Ch Stay', choice_PE_3),
('Stay Cur Rew', choice_PE_3_reward_current),
('Stay Prev Rew', choice_PE_3_reward_prev),
('Ch x Rew ', rew_ch_3), (' Prev Ch x Prev Rew', prev_choice_3_lr),
('Prev Rew', prev_reward_3), ('Prev Ch', prev_choice_3),
('ones', ones_3)
])
X_3 = np.vstack(predictors_all.values()).T[:trials_3, :].astype(float)
rank = np.linalg.matrix_rank(X_3)
print(rank)
n_predictors = X_3.shape[1]
print(n_predictors)
y_3 = firing_rates_3.reshape(
[len(firing_rates_3),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_3, X_3)
C_3.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_3.append(
re._CPD(X_3, y_3).reshape(n_neurons, n_timepoints, n_predictors))
C_1 = np.concatenate(C_1, 1)
C_2 = np.concatenate(C_2, 1)
C_3 = np.concatenate(C_3, 1)
cpd_1 = np.nanmean(np.concatenate(cpd_1, 0), axis=0)
cpd_2 = np.nanmean(np.concatenate(cpd_2, 0), axis=0)
cpd_3 = np.nanmean(np.concatenate(cpd_3, 0), axis=0)
cpd = np.mean([cpd_1, cpd_2, cpd_3], 0)
c = wes.Darjeeling2_5.mpl_colors + wes.Mendl_4.mpl_colors + wes.GrandBudapest1_4.mpl_colors + wes.Moonrise1_5.mpl_colors
j = 0
plt.figure()
pred = list(predictors_all.keys())
pred = pred[2:-1]
for ii, i in enumerate(cpd.T[2:-1]):
plt.plot(i, color=c[j], label=pred[j])
j += 1
plt.legend()
sns.despine()
C_2_inf = [~np.isinf(C_2[0]).any(axis=1)]
C_2_nan = [~np.isnan(C_2[0]).any(axis=1)]
C_3_inf = [~np.isinf(C_3[0]).any(axis=1)]
C_3_nan = [~np.isnan(C_3[0]).any(axis=1)]
C_1_inf = [~np.isinf(C_1[0]).any(axis=1)]
C_1_nan = [~np.isnan(C_1[0]).any(axis=1)]
nans = np.asarray(C_1_inf) & np.asarray(C_1_nan) & np.asarray(
C_3_inf) & np.asarray(C_3_nan) & np.asarray(C_2_inf) & np.asarray(
C_2_nan)
C_1 = C_1[:, nans[0], :]
C_2 = C_2[:, nans[0], :]
C_3 = C_3[:, nans[0], :]
preds = np.arange(len(list(predictors_all.keys())))
coef_1 = np.tile(preds, 11)
coef_2 = np.concatenate((preds, np.roll(preds,1), np.roll(preds,2),np.roll(preds,3), np.roll(preds,4),np.roll(preds,5),\
np.roll(preds,6), np.roll(preds,7), np.roll(preds,8),np.roll(preds,9), np.roll(preds,10)))
m = 0
l = 0
plt.figure(figsize=(10, 10))
for c_1, c_2 in zip(coef_1, coef_2):
title = list(predictors_all.keys())[c_1] + ' ' + 'on' + ' ' + list(
predictors_all.keys())[c_2]
m += 1
l += 1
if m == 10:
plt.savefig('/Users/veronikasamborska/Desktop/runs/within' + area +
str(l) + '.png')
plt.figure(figsize=(10, 10))
m -= 9
C_1_rew = C_1[c_1]
C_2_rew = C_2[c_1]
C_3_rew = C_3[c_1]
C_1_rew_count = C_1[c_2]
C_2_rew_count = C_2[c_2]
C_3_rew_count = C_3[c_2]
reward_times_to_choose = np.asarray([20, 24, 35, 41])
C_1_rew_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
C_2_rew_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
C_3_rew_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
j = 0
for i in reward_times_to_choose:
if i == reward_times_to_choose[0]:
C_1_rew_proj[:, j] = np.mean(C_1_rew[:, i - 20:i], 1)
C_2_rew_proj[:, j] = np.mean(C_2_rew[:, i - 20:i], 1)
C_3_rew_proj[:, j] = np.mean(C_3_rew[:, i - 20:i], 1)
elif i == reward_times_to_choose[1] or i == reward_times_to_choose[
2]:
C_1_rew_proj[:, j] = np.mean(C_1_rew[:, i - 5:i + 5], 1)
C_2_rew_proj[:, j] = np.mean(C_2_rew[:, i - 5:i + 5], 1)
C_3_rew_proj[:, j] = np.mean(C_3_rew[:, i - 5:i + 5], 1)
elif i == reward_times_to_choose[3]:
C_1_rew_proj[:, j] = np.mean(C_1_rew[:, i:i + 5], 1)
C_2_rew_proj[:, j] = np.mean(C_2_rew[:, i:i + 5], 1)
C_3_rew_proj[:, j] = np.mean(C_3_rew[:, i:i + 5], 1)
j += 1
C_1_rew_count_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
C_2_rew_count_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
C_3_rew_count_proj = np.ones(
(C_1_rew.shape[0], reward_times_to_choose.shape[0] + 1))
j = 0
for i in reward_times_to_choose:
if i == reward_times_to_choose[0]:
C_1_rew_count_proj[:, j] = np.mean(C_1_rew_count[:, i - 20:i],
1)
C_2_rew_count_proj[:, j] = np.mean(C_2_rew_count[:, i - 20:i],
1)
C_3_rew_count_proj[:, j] = np.mean(C_3_rew_count[:, i - 20:i],
1)
elif i == reward_times_to_choose[1] or i == reward_times_to_choose[
2]:
C_1_rew_count_proj[:,
j] = np.mean(C_1_rew_count[:, i - 5:i + 5],
1)
C_2_rew_count_proj[:,
j] = np.mean(C_2_rew_count[:, i - 5:i + 5],
1)
C_3_rew_count_proj[:,
j] = np.mean(C_3_rew_count[:, i - 5:i + 5],
1)
elif i == reward_times_to_choose[3]:
C_1_rew_count_proj[:, j] = np.mean(C_1_rew_count[:, i:i + 5],
1)
C_2_rew_count_proj[:, j] = np.mean(C_2_rew_count[:, i:i + 5],
1)
C_3_rew_count_proj[:, j] = np.mean(C_3_rew_count[:, i:i + 5],
1)
j += 1
cpd_1_2_rew, cpd_1_2_rew_var = regression_code_session(
C_1_rew_count, C_1_rew_proj)
cpd_1_3_rew, cpd_1_3_rew_var = regression_code_session(
C_2_rew_count, C_2_rew_proj)
cpd_2_3_rew, cpd_2_3_rew_var = regression_code_session(
C_3_rew_count, C_3_rew_proj)
rew_to_count_cpd = (cpd_1_2_rew + cpd_1_3_rew + cpd_2_3_rew) / np.sqrt(
(cpd_1_2_rew_var + cpd_1_3_rew_var + cpd_2_3_rew_var))
j = 0
plt.subplot(5, 2, m)
for i in rew_to_count_cpd[:-1]:
plt.plot(i, color=c[j], label=str(j))
j += 1
# plt.legend()
plt.title(area + ' ' + str(title))
sns.despine()
plt.tight_layout()
def within_taks_codes(data, area='HP', perm=5):
dm = data['DM'][0]
firing = data['Data'][0]
C = []
cpd = []
cpd_perm_p = []
for s, sess in enumerate(dm):
cpd_perm = [[] for i in range(perm)
] # To store permuted predictor loadings for each session.
runs_list = []
runs_list.append(0)
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
state = DM[:, 0]
choices = DM[:, 1]
reward = DM[:, 2]
reward_2_ago = 0.5 - reward[1:-2]
reward_3_ago = 0.5 - reward[:-3]
reward_prev = 0.5 - reward[2:-1]
reward_current = reward[3:]
# reward_o_1_ago = np.asarray(reward_prev)
# reward_o_2_ago = np.asarray(reward_2_ago)
# reward_o_3_ago = np.asarray(reward_3_ago)
firing_rates = firing_rates[3:]
choices_2_ago = 0.5 - choices[1:-2]
choices_3_ago = 0.5 - choices[:-3]
choices_prev = 0.5 - choices[2:-1]
choices_current = choices[3:]
state = state[3:]
cum_reward_orth = np.vstack(
[reward_current, np.ones(len(reward_current))]).T
xt = np.linalg.pinv(cum_reward_orth)
identity = np.identity(len(reward_current))
id_x = (identity - np.matmul(cum_reward_orth, xt))
# choice_o_1_ago = np.matmul(id_x, np.asarray(choices_prev))
# choice_o_2_ago = np.matmul(id_x, np.asarray(choices_2_ago))
# choice_o_3_ago = np.matmul(id_x, np.asarray(choices_3_ago))
ch_rew_int_1 = choices_prev * reward_prev
ch_rew_int_2 = choices_2_ago * reward_2_ago
ch_rew_int_3 = choices_3_ago * reward_3_ago
ones = np.ones(len(choices_3_ago))
predictors_all = OrderedDict([('Reward', reward_current),
('Choice', choices_current),
('1 ago Outcome', reward_prev),
('2 ago Outcome', reward_2_ago),
('3 ago Outcome', reward_3_ago),
('1 ago Choice', choices_prev),
('2 ago Choice', choices_2_ago),
('3 ago Choice', choices_3_ago),
('1 Rew x Choice', ch_rew_int_1),
('2 Rew x Choice', ch_rew_int_2),
('3 Rew x Choice', ch_rew_int_3),
('ones', ones)])
X = np.vstack(
predictors_all.values()).T[:len(choices_current), :].astype(float)
rank = np.linalg.matrix_rank(X)
print(rank)
print(X.shape[1])
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
if perm:
for i in range(perm):
y_perm = np.roll(y, np.random.randint(len(y)), axis=0)
cpd_temp = re._CPD(X, y_perm).reshape(n_neurons, n_timepoints,
n_predictors)
cpd_perm[i].append(np.nanmean(cpd_temp, axis=0))
cpd_perm_p.append(np.percentile(cpd_perm, 95, axis=0))
if perm: # Evaluate P values.
cpd_perm_pval = np.mean(cpd_perm_p, 0)[0]
#cpd_perm_p = np.percentile(cpd_perm,95, axis = 0)
C = np.concatenate(C, 1)
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
plt.figure()
pred = list(predictors_all.keys())
array_pvals = np.ones((cpd.shape[0], cpd.shape[1]))
for i in range(cpd.shape[1]):
array_pvals[(np.where(cpd[:, i] > cpd_perm_pval[:, i])[0]), i] = 0.05
ymax = np.max(cpd[:, 2:-1].T)
t = np.arange(0, 121)
c = wes.Darjeeling2_5.mpl_colors + wes.Mendl_4.mpl_colors + wes.GrandBudapest1_4.mpl_colors + wes.Moonrise1_5.mpl_colors
for i in np.arange(cpd.shape[1]):
if i > 1 and i < cpd.shape[1] - 1:
plt.plot(cpd[:, i], label=pred[i], color=c[i])
y = ymax * (1 + 0.04 * i)
p_vals = array_pvals[:, i]
t05 = t[p_vals == 0.05]
plt.plot(t05,
np.ones(t05.shape) * y,
'.',
markersize=5,
color=c[i])
plt.legend()
plt.ylabel('CPD')
plt.xlabel('Time in Trial')
plt.xticks([24, 35, 42], ['I', 'C', 'R'])
plt.legend()
sns.despine()
plt.title(area)
def sequence_rewards_errors_regression(data, perm=True):
dm = data['DM'][0]
firing = data['Data'][0]
C = []
cpd = []
for s, sess in enumerate(dm):
runs_list = []
runs_list.append(0)
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1]
reward = DM[:, 2]
state = DM[:, 0]
cum_error = []
err = 0
for r in reward:
if r == 0:
err += 1
else:
err = 0
cum_error.append(err)
cum_reward = []
for r in reward:
if r == 1:
err += 1
else:
err = 0
cum_reward.append(err)
ones = np.ones(len(reward))
predictors_all = OrderedDict([('Reward', reward), ('Choice', choices),
('State', state), ('Errors', cum_error),
('Rewards', cum_reward), ('ones', ones)])
X = np.vstack(
predictors_all.values()).T[:len(choices), :].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
C = np.concatenate(C, 1)
high_loadings_rewards = np.where(abs(np.mean(C[4, :, :20], 1)) > 2.5)[0]
high_loadings_errors = np.where(abs(np.mean(C[3, :, :20], 1)) > 2.5)[0]
return high_loadings_errors, high_loadings_rewards
def regression_latent_state(experiment, experiment_sim_Q4_values):
C_1 = []
C_coef = []
cpd_1 = []
# Finding correlation coefficients for task 1
for s,session in enumerate(experiment):
aligned_spikes= session.aligned_rates[:]
if aligned_spikes.shape[1] > 0: # sessions with neurons?
n_trials, n_neurons, n_timepoints = aligned_spikes.shape
#aligned_spikes = np.mean(aligned_spikes, axis = 2)
# Getting out task indicies
task = session.trial_data['task']
forced_trials = session.trial_data['forced_trial']
non_forced_array = np.where(forced_trials == 0)[0]
task_non_forced = task[non_forced_array]
task_1 = np.where(task_non_forced == 1)[0]
task_2 = np.where(task_non_forced == 2)[0]
predictor_A_Task_1, predictor_A_Task_2, predictor_A_Task_3,\
predictor_B_Task_1, predictor_B_Task_2, predictor_B_Task_3, reward,\
predictor_a_good_task_1,predictor_a_good_task_2, predictor_a_good_task_3 = re.predictors_pokes(session)
# Getting out task indicies
Q4 = experiment_sim_Q4_values[s]
forced_trials = session.trial_data['forced_trial']
outcomes = session.trial_data['outcomes']
choices = session.trial_data['choices']
non_forced_array = np.where(forced_trials == 0)[0]
choices = choices[non_forced_array]
Q4 = Q4[non_forced_array]
aligned_spikes = aligned_spikes[:len(choices),:]
outcomes = outcomes[non_forced_array]
# Getting out task indicies
ones = np.ones(len(choices))
choices = choices[:len(task_1)]
outcomes = outcomes[:len(task_1)]
latent_state = np.ones(len(task_1))
latent_state[predictor_a_good_task_1] = -1
ones = ones[:len(task_1)]
aligned_spikes = aligned_spikes[:len(task_1)]
Q4 = Q4[:len(task_1)]
choice_Q4 = choices*Q4
predictors = OrderedDict([#('latent_state',latent_state),
('choice', choices),
('reward', outcomes),
('Q4', Q4),
('choice_Q4',choice_Q4),
('ones', ones)])
X = np.vstack(predictors.values()).T[:len(choices),:].astype(float)
n_predictors = X.shape[1]
y = aligned_spikes.reshape([len(aligned_spikes),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
ols = LinearRegression(copy_X = True,fit_intercept= True)
ols.fit(X,y)
C_coef.append(ols.coef_.reshape(n_neurons, n_predictors,n_timepoints)) # Predictor loadings
C_1.append(tstats.reshape(n_predictors,n_neurons,n_timepoints)) # Predictor loadings
cpd_1.append(re._CPD(X,y).reshape(n_neurons,n_timepoints, n_predictors))
C_1 = np.concatenate(C_1, axis = 1) #
C_coef = np.concatenate(C_coef, axis = 0) #
cpd_1 = np.nanmean(np.concatenate(cpd_1,0), axis = 0)
C_2 = []
C_coef_2 = []
cpd_2 = []
# Finding correlation coefficients for task 1
for s,session in enumerate(experiment):
aligned_spikes= session.aligned_rates[:]
if aligned_spikes.shape[1] > 0: # sessions with neurons?
n_trials, n_neurons, n_timepoints = aligned_spikes.shape
#aligned_spikes = np.mean(aligned_spikes, axis = 2)
Q4 = experiment_sim_Q4_values[s]
# Getting out task indicies
task = session.trial_data['task']
forced_trials = session.trial_data['forced_trial']
non_forced_array = np.where(forced_trials == 0)[0]
task_non_forced = task[non_forced_array]
task_1 = np.where(task_non_forced == 1)[0]
task_2 = np.where(task_non_forced == 2)[0]
predictor_A_Task_1, predictor_A_Task_2, predictor_A_Task_3,\
predictor_B_Task_1, predictor_B_Task_2, predictor_B_Task_3, reward,\
predictor_a_good_task_1,predictor_a_good_task_2, predictor_a_good_task_3 = re.predictors_pokes(session)
# Getting out task indicies
forced_trials = session.trial_data['forced_trial']
outcomes = session.trial_data['outcomes']
choices = session.trial_data['choices']
non_forced_array = np.where(forced_trials == 0)[0]
Q4 = Q4[non_forced_array]
choices = choices[non_forced_array]
aligned_spikes = aligned_spikes[:len(choices),:]
outcomes = outcomes[non_forced_array]
# Getting out task indicies
ones = np.ones(len(choices))
choices = choices[len(task_1):len(task_1)+len(task_2)]
latent_state = np.ones(len(choices))
latent_state[predictor_a_good_task_2] = -1
outcomes = outcomes[len(task_1):len(task_1)+len(task_2)]
ones = ones[len(task_1):len(task_1)+len(task_2)]
aligned_spikes = aligned_spikes[len(task_1):len(task_1)+len(task_2)]
Q4 = Q4[len(task_1):len(task_1)+len(task_2)]
choice_Q4 = choices*Q4
predictors = OrderedDict([#('latent_state',latent_state),
('choice', choices),
('reward', outcomes),
('Q4',Q4),
('choice_Q4',choice_Q4),
('ones', ones)])
X = np.vstack(predictors.values()).T[:len(choices),:].astype(float)
n_predictors = X.shape[1]
y = aligned_spikes.reshape([len(aligned_spikes),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_2.append(tstats.reshape(n_predictors,n_neurons,n_timepoints)) # Predictor loadings
ols = LinearRegression(copy_X = True,fit_intercept= True)
ols.fit(X,y)
C_coef_2.append(ols.coef_.reshape(n_neurons, n_predictors,n_timepoints)) # Predictor loadings
cpd_2.append(re._CPD(X,y).reshape(n_neurons,n_timepoints, n_predictors))
C_2 = np.concatenate(C_2, axis = 1) # Population CPD is mean over neurons.
C_coef_2 = np.concatenate(C_coef_2, axis = 0) # Population CPD is mean over neurons.
cpd_2 = np.nanmean(np.concatenate(cpd_2,0), axis = 0)
C_3 = []
C_coef_3 = []
cpd_3 = []
# Finding correlation coefficients for task 1
for s,session in enumerate(experiment):
aligned_spikes= session.aligned_rates[:]
if aligned_spikes.shape[1] > 0: # sessions with neurons?
n_trials, n_neurons, n_timepoints = aligned_spikes.shape
#aligned_spikes = np.mean(aligned_spikes, axis = 2)
# Getting out task indicies
task = session.trial_data['task']
forced_trials = session.trial_data['forced_trial']
non_forced_array = np.where(forced_trials == 0)[0]
task_non_forced = task[non_forced_array]
task_1 = np.where(task_non_forced == 1)[0]
task_2 = np.where(task_non_forced == 2)[0]
Q4 = experiment_sim_Q4_values[s]
predictor_A_Task_1, predictor_A_Task_2, predictor_A_Task_3,\
predictor_B_Task_1, predictor_B_Task_2, predictor_B_Task_3, reward,\
predictor_a_good_task_1,predictor_a_good_task_2, predictor_a_good_task_3 = re.predictors_pokes(session)
# Getting out task indicies
forced_trials = session.trial_data['forced_trial']
outcomes = session.trial_data['outcomes']
choices = session.trial_data['choices']
non_forced_array = np.where(forced_trials == 0)[0]
Q4 = Q4[non_forced_array]
choices = choices[non_forced_array]
aligned_spikes = aligned_spikes[:len(choices),:]
outcomes = outcomes[non_forced_array]
# Getting out task indicies
ones = np.ones(len(choices))
choices = choices[len(task_1)+len(task_2):]
latent_state = np.ones(len(choices))
latent_state[predictor_a_good_task_3] = -1
outcomes = outcomes[len(task_1)+len(task_2):]
ones = ones[len(task_1)+len(task_2):]
Q4 = Q4[len(task_1)+len(task_2):]
choice_Q4 = choices*Q4
aligned_spikes = aligned_spikes[len(task_1)+len(task_2):]
predictors = OrderedDict([#('latent_state', latent_state),
('choice', choices),
('reward', outcomes),
('Q4', Q4),
('choice_Q4',choice_Q4),
('ones', ones)])
X = np.vstack(predictors.values()).T[:len(choices),:].astype(float)
n_predictors = X.shape[1]
y = aligned_spikes.reshape([len(aligned_spikes),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_3.append(tstats.reshape(n_predictors,n_neurons,n_timepoints)) # Predictor loadings
ols = LinearRegression(copy_X = True,fit_intercept= True)
ols.fit(X,y)
C_coef_3.append(ols.coef_.reshape(n_neurons,n_timepoints, n_predictors)) # Predictor loadings
cpd_3.append(re._CPD(X,y).reshape(n_neurons,n_timepoints, n_predictors))
C_3 = np.concatenate(C_3, axis = 1) # Population CPD is mean over neurons.
C_coef_3 = np.concatenate(C_coef_3, axis = 0) # Population CPD is mean over neurons.
cpd_3 = np.nanmean(np.concatenate(cpd_3,0), axis = 0)
return C_1, C_2, C_3, C_coef,C_coef_2,C_coef_3,cpd_1,cpd_2,cpd_3,predictors
def sequence_rewards_errors_regression_generalisation(data,
perm=True,
area='HP_',
interactions=True,
a=True):
dm = data['DM'][0]
firing = data['Data'][0]
C_1 = []
cpd_1 = []
C_2 = []
cpd_2 = []
C_3 = []
cpd_3 = []
if perm:
C_1_perm = [[] for i in range(perm)]
C_2_perm = [[] for i in range(perm)]
C_3_perm = [[] for i in range(perm)]
cpd_perm_all = [[] for i in range(perm)]
for s, sess in enumerate(dm):
runs_list = []
runs_list.append(0)
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1]
# choices[np.where(choices ==0)[0]] = -1
reward = DM[:, 2]
task = DM[:, 5]
task_1 = np.where(task == 1)[0]
task_2 = np.where(task == 2)[0]
task_3 = np.where(task == 3)[0]
state = DM[:, 0]
correct = np.where(state == choices)[0]
incorrect = np.where(state != choices)[0]
cum_error = []
runs_list_corr = []
runs_list_incorr = []
err = 0
for r in reward:
if r == 0:
err += 1
else:
err = 0
cum_error.append(err)
cum_reward = []
for r in reward:
if r == 1:
err += 1
else:
err = 0
cum_reward.append(err)
run = 0
for c, ch in enumerate(choices):
if c > 0:
if choices[c] == choices[c - 1]:
run += 1
elif choices[c] != choices[c - 1]:
run = 0
runs_list.append(run)
corr_run = 0
run_ind_c = []
for c, ch in enumerate(choices):
if c > 0 and c in correct:
if choices[c] == choices[c - 1]:
if corr_run == 0:
run_ind_c.append(c)
corr_run += 1
elif choices[c] != choices[c - 1]:
corr_run = 0
else:
corr_run = 0
runs_list_corr.append(corr_run)
incorr_run = 0
run_ind_inc = []
for c, ch in enumerate(choices):
if c > 0 and c in incorrect:
if choices[c] == choices[c - 1]:
if incorr_run == 0:
run_ind_inc.append(c)
incorr_run += 1
elif choices[c] != choices[c - 1]:
incorr_run = 0
else:
incorr_run = 0
runs_list_incorr.append(incorr_run)
choices_a = np.where(choices == 1)[0]
choices_b = np.where(choices == 0)[0]
a_cum_rew = np.copy(np.asarray(np.asarray(cum_reward)))
b_cum_rew = np.copy(np.asarray(np.asarray(cum_reward)))
a_cum_rew[choices_b] = 0
b_cum_rew[choices_a] = 0
a_cum_error = np.copy(np.asarray(np.asarray(cum_error)))
b_cum_error = np.copy(np.asarray(np.asarray(cum_error)))
a_cum_error[choices_b] = 0
b_cum_error[choices_a] = 0
ones = np.ones(len(reward))
reward_1 = reward[task_1]
choices_1 = choices[task_1]
cum_error_1 = np.asarray(cum_error)[task_1]
cum_reward_1 = np.asarray(cum_reward)[task_1]
cum_error_1_a = np.asarray(a_cum_error)[task_1]
cum_error_1_b = np.asarray(b_cum_error)[task_1]
cum_reward_1_a = np.asarray(a_cum_rew)[task_1]
cum_reward_1_b = np.asarray(b_cum_rew)[task_1]
ones_1 = ones[task_1]
cum_error_1_ch = cum_error_1 * choices_1
cum_rew_1_ch = cum_reward_1 * choices_1
firing_rates_1 = firing_rates[task_1]
int_rew_ch_1 = reward_1 * choices_1
if interactions == True:
predictors_all = OrderedDict([
('Reward', reward_1), ('Choice', choices_1),
('Errors', cum_error_1), ('Rewards', cum_reward_1),
('Choice x Cum Error', cum_error_1_ch),
('Choice x Cum Reward', cum_rew_1_ch),
('Choice x Reward', int_rew_ch_1), ('ones', ones_1)
])
else:
predictors_all = OrderedDict([('Reward', reward_1),
('Choice', choices_1),
('Errors A', cum_error_1_a),
('Errors B', cum_error_1_b),
('Rewards A', cum_reward_1_a),
('Rewards B', cum_reward_1_b),
('Choice x Reward', int_rew_ch_1),
('ones', ones_1)])
X_1 = np.vstack(
predictors_all.values()).T[:len(choices_1), :].astype(float)
rank = np.linalg.matrix_rank(X_1)
# print(rank)
# print(X_1.shape[1])
n_predictors = X_1.shape[1]
y_1 = firing_rates_1.reshape(
[len(firing_rates_1),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_1, X_1)
C_1.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_1.append(
re._CPD(X_1, y_1).reshape(n_neurons, n_timepoints, n_predictors))
reward_2 = reward[task_2]
choices_2 = choices[task_2]
cum_error_2 = np.asarray(cum_error)[task_2]
cum_reward_2 = np.asarray(cum_reward)[task_2]
ones_2 = ones[task_2]
cum_error_2_ch = cum_error_2 * choices_2
cum_rew_2_ch = cum_reward_2 * choices_2
int_rew_ch_2 = reward_2 * choices_2
cum_error_2_a = np.asarray(a_cum_error)[task_2]
cum_error_2_b = np.asarray(b_cum_error)[task_2]
cum_reward_2_a = np.asarray(a_cum_rew)[task_2]
cum_reward_2_b = np.asarray(b_cum_rew)[task_2]
firing_rates_2 = firing_rates[task_2]
if interactions == True:
predictors_all = OrderedDict([
('Reward', reward_2), ('Choice', choices_2),
('Errors', cum_error_2), ('Rewards', cum_reward_2),
('Choice x Cum Error', cum_error_2_ch),
('Choice x Cum Reward', cum_rew_2_ch),
('Choice x Reward', int_rew_ch_2), ('ones', ones_2)
])
else:
predictors_all = OrderedDict([('Reward', reward_2),
('Choice', choices_2),
('Errors A', cum_error_2_a),
('Errors B', cum_error_2_b),
('Rewards A', cum_reward_2_a),
('Rewards B', cum_reward_2_b),
('Choice x Reward', int_rew_ch_2),
('ones', ones_2)])
X_2 = np.vstack(
predictors_all.values()).T[:len(choices_2), :].astype(float)
y_2 = firing_rates_2.reshape(
[len(firing_rates_2),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_2, X_2)
C_2.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_2.append(
re._CPD(X_2, y_2).reshape(n_neurons, n_timepoints, n_predictors))
reward_3 = reward[task_3]
choices_3 = choices[task_3]
cum_error_3 = np.asarray(cum_error)[task_3]
cum_reward_3 = np.asarray(cum_reward)[task_3]
ones_3 = ones[task_3]
cum_error_3_ch = cum_error_3 * choices_3
cum_rew_3_ch = cum_reward_3 * choices_3
int_rew_ch_3 = reward_3 * choices_3
cum_error_3_a = np.asarray(a_cum_error)[task_3]
cum_error_3_b = np.asarray(b_cum_error)[task_3]
cum_reward_3_a = np.asarray(a_cum_rew)[task_3]
cum_reward_3_b = np.asarray(b_cum_rew)[task_3]
firing_rates_3 = firing_rates[task_3]
if interactions == True:
predictors_all = OrderedDict([
('Reward', reward_3), ('Choice', choices_3),
('Errors', cum_error_3), ('Rewards', cum_reward_3),
('Choice x Cum Error', cum_error_3_ch),
('Choice x Cum Reward', cum_rew_3_ch),
('Choice x Reward', int_rew_ch_3), ('ones', ones_3)
])
else:
predictors_all = OrderedDict([('Reward', reward_3),
('Choice', choices_3),
('Errors A', cum_error_3_a),
('Errors B', cum_error_3_b),
('Rewards A', cum_reward_3_a),
('Rewards B', cum_reward_3_b),
('Choice x Reward', int_rew_ch_3),
('ones', ones_3)])
X_3 = np.vstack(
predictors_all.values()).T[:len(choices_3), :].astype(float)
y_3 = firing_rates_3.reshape(
[len(firing_rates_3),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_3, X_3)
C_3.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_3.append(
re._CPD(X_3, y_3).reshape(n_neurons, n_timepoints, n_predictors))
if perm:
for i in range(perm):
X_perm_1 = np.roll(X_1, np.random.randint(len(X_1)), axis=0)
tstats = reg_f.regression_code(y_1, X_perm_1)
C_1_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm_1 = re._CPD(X_perm_1,
y_1).reshape(n_neurons, n_timepoints,
n_predictors)
X_perm_2 = np.roll(X_2, np.random.randint(len(X_2)), axis=0)
tstats = reg_f.regression_code(y_2, X_perm_2)
C_2_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm_2 = re._CPD(X_perm_2,
y_2).reshape(n_neurons, n_timepoints,
n_predictors)
X_perm_3 = np.roll(X_3, np.random.randint(len(X_3)), axis=0)
tstats = reg_f.regression_code(y_3, X_perm_3)
C_3_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm_3 = re._CPD(X_perm_3,
y_3).reshape(n_neurons, n_timepoints,
n_predictors)
cpd_perm_all[i].append(
np.nanmean([cpd_perm_1, cpd_perm_2, cpd_perm_3], 0))
cpd_perm_all = np.stack(
[np.mean(np.concatenate(cpd_i, 0), 0) for cpd_i in cpd_perm_all], 0)
cpd_1 = np.nanmean(np.concatenate(cpd_1, 0), axis=0)
C_1 = np.concatenate(C_1, 1)
cpd_2 = np.nanmean(np.concatenate(cpd_2, 0), axis=0)
C_2 = np.concatenate(C_2, 1)
cpd_3 = np.nanmean(np.concatenate(cpd_3, 0), axis=0)
C_3 = np.concatenate(C_3, 1)
cpds_true = np.mean([cpd_1, cpd_2, cpd_3], 0)
pal_c = sns.cubehelix_palette(8, start=2, rot=0, dark=0, light=.95)
c = wes.Darjeeling2_5.mpl_colors + wes.Mendl_4.mpl_colors + wes.GrandBudapest1_4.mpl_colors + wes.Moonrise1_5.mpl_colors
cpd_perm_all = np.max(np.percentile(cpd_perm_all, 95, axis=0), 0)
j = 0
plt.figure()
for i in cpds_true.T[:-1]:
plt.plot(i, color=c[j], label=list(predictors_all.keys())[j])
plt.hlines(cpd_perm_all[j], xmin=0, xmax=63, color=c[j], linestyle=':')
j += 1
plt.legend()
sns.despine()
plt.title(area + 'CPDs')
if interactions == True:
X_nan, firing_rates_1_inf_rew,firing_rates_2_inf_rew,firing_rates_3_inf_rew,firing_rates_1_inf_error,firing_rates_2_inf_error,\
firing_rates_3_inf_error,firing_rates_1_inf_rew_int,firing_rates_2_inf_rew_int,firing_rates_3_inf_rew_int,firing_rates_1_inf_error_int,\
firing_rates_2_inf_error_int,firing_rates_3_inf_error_int = find_coefficients(C_1,C_2,C_3,interactions = interactions, a = a)
X_1_rew = X_nan[:, :5]
X_1_rew_int = X_nan[:, 5:10]
X_1_error = X_nan[:, 10:15]
X_1_error_int = X_nan[:, 15:20]
X_2_rew = X_nan[:, 20:25]
X_2_rew_int = X_nan[:, 25:30]
X_2_error = X_nan[:, 30:35]
X_2_error_int = X_nan[:, 35:40]
X_3_rew = X_nan[:, 40:45]
X_3_rew_int = X_nan[:, 45:50]
X_3_error = X_nan[:, 50:55]
X_3_error_int = X_nan[:, 55:60]
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_rew[:,i],X_2_rew[:,i], color = 'red',label = 'Reward')
# #sns.regplot(X_1_rew[:,i],X_3_rew[:,i], color = 'black')
# #sns.regplot(X_3_rew[:,i],X_2_rew[:,i], color = 'grey')
# corr = np.mean([np.corrcoef(X_1_rew[:,i],X_2_rew[:,i])[0,1],np.corrcoef(X_1_rew[:,i],X_3_rew[:,i])[0,1],np.corrcoef(X_2_rew[:,i],X_3_rew[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
# plt.legend()
# sns.despine()
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_rew_int[:,i],X_2_rew_int[:,i], color = 'grey', label = 'Reward Interaction')
# corr = np.mean([np.corrcoef(X_1_rew_int[:,i],X_2_rew_int[:,i])[0,1],np.corrcoef(X_1_rew_int[:,i],X_3_rew_int[:,i])[0,1],np.corrcoef(X_2_rew_int[:,i],X_3_rew_int[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
# plt.legend()
# sns.despine()
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_error[:,i],X_2_error[:,i], color = 'purple', label = 'Error')
# corr = np.mean([np.corrcoef(X_1_error[:,i],X_2_error[:,i])[0,1],np.corrcoef(X_1_error[:,i],X_3_error[:,i])[0,1],np.corrcoef(X_2_error[:,i],X_3_error[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_error_int[:,i],X_2_error_int[:,i], color = 'purple', label = 'Error')
# corr = np.mean([np.corrcoef(X_1_error_int[:,i],X_2_error_int[:,i])[0,1],np.corrcoef(X_1_error_int[:,i],X_3_error_int[:,i])[0,1],np.corrcoef(X_2_error_int[:,i],X_3_error_int[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
# plt.legend()
# sns.despine()
cpd_1_2_rew = re._CPD(X_1_rew, firing_rates_2_inf_rew)
cpd_1_3_rew = re._CPD(X_1_rew, firing_rates_3_inf_rew)
cpd_2_1_rew = re._CPD(X_2_rew, firing_rates_1_inf_rew)
cpd_2_3_rew = re._CPD(X_2_rew, firing_rates_3_inf_rew)
cpd_3_1_rew = re._CPD(X_3_rew, firing_rates_1_inf_rew)
cpd_3_2_rew = re._CPD(X_3_rew, firing_rates_2_inf_rew)
cpd_1_2_error = re._CPD(X_1_error, firing_rates_2_inf_error)
cpd_1_3_error = re._CPD(X_1_error, firing_rates_3_inf_error)
cpd_2_1_error = re._CPD(X_2_error, firing_rates_1_inf_error)
cpd_2_3_error = re._CPD(X_2_error, firing_rates_3_inf_error)
cpd_3_1_error = re._CPD(X_3_error, firing_rates_1_inf_error)
cpd_3_2_error = re._CPD(X_3_error, firing_rates_2_inf_error)
cpd_1_2_rew_int = re._CPD(X_1_rew_int, firing_rates_2_inf_rew_int)
cpd_1_3_rew_int = re._CPD(X_1_rew_int, firing_rates_3_inf_rew_int)
cpd_2_1_rew_int = re._CPD(X_2_rew_int, firing_rates_1_inf_rew_int)
cpd_2_3_rew_int = re._CPD(X_2_rew_int, firing_rates_3_inf_rew_int)
cpd_3_1_rew_int = re._CPD(X_3_rew_int, firing_rates_1_inf_rew_int)
cpd_3_2_rew_int = re._CPD(X_3_rew_int, firing_rates_2_inf_rew_int)
cpd_1_2_error_int = re._CPD(X_1_error_int,
firing_rates_2_inf_error_int)
cpd_1_3_error_int = re._CPD(X_1_error_int,
firing_rates_3_inf_error_int)
cpd_2_1_error_int = re._CPD(X_2_error_int,
firing_rates_1_inf_error_int)
cpd_2_3_error_int = re._CPD(X_2_error_int,
firing_rates_3_inf_error_int)
cpd_3_1_error_int = re._CPD(X_3_error_int,
firing_rates_1_inf_error_int)
cpd_3_2_error_int = re._CPD(X_3_error_int,
firing_rates_2_inf_error_int)
cpd_rew_int = np.nanmean([
cpd_1_2_rew_int, cpd_1_3_rew_int, cpd_2_1_rew_int, cpd_2_3_rew_int,
cpd_3_1_rew_int, cpd_3_2_rew_int
], 0)
cpd_error_int = np.nanmean([
cpd_1_2_error_int, cpd_1_3_error_int, cpd_2_1_error_int,
cpd_2_3_error_int, cpd_3_1_error_int, cpd_3_2_error_int
], 0)
else:
X_nan, firing_rates_1_inf_rew,firing_rates_2_inf_rew,firing_rates_3_inf_rew,firing_rates_1_inf_error,firing_rates_2_inf_error,\
firing_rates_3_inf_error = find_coefficients(C_1,C_2,C_3,interactions = interactions, a = a)
X_1_rew = X_nan[:, :5]
X_1_error = X_nan[:, 5:10]
X_2_rew = X_nan[:, 10:15]
X_2_error = X_nan[:, 15:20]
X_3_rew = X_nan[:, 20:25]
X_3_error = X_nan[:, 25:30]
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_rew[:,i],X_2_rew[:,i], color = 'red',label = 'Reward')
# #sns.regplot(X_1_rew[:,i],X_3_rew[:,i], color = 'black')
# #sns.regplot(X_3_rew[:,i],X_2_rew[:,i], color = 'grey')
# corr = np.mean([np.corrcoef(X_1_rew[:,i],X_2_rew[:,i])[0,1],np.corrcoef(X_1_rew[:,i],X_3_rew[:,i])[0,1],np.corrcoef(X_2_rew[:,i],X_3_rew[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
# plt.legend()
# plt.figure()
# for i in range(4):
# plt.subplot(2,2,i+1)
# sns.regplot(X_1_error[:,i],X_2_error[:,i], color = 'purple', label = 'Error')
# corr = np.mean([np.corrcoef(X_1_error[:,i],X_2_error[:,i])[0,1],np.corrcoef(X_1_error[:,i],X_3_error[:,i])[0,1],np.corrcoef(X_2_error[:,i],X_3_error[:,i])[0,1]])
# plt.annotate(np.round(corr,2),(1,1.5))
cpd_1_2_rew = re._CPD(X_1_rew, firing_rates_2_inf_rew)
cpd_1_3_rew = re._CPD(X_1_rew, firing_rates_3_inf_rew)
cpd_2_1_rew = re._CPD(X_2_rew, firing_rates_1_inf_rew)
cpd_2_3_rew = re._CPD(X_2_rew, firing_rates_3_inf_rew)
cpd_3_1_rew = re._CPD(X_3_rew, firing_rates_1_inf_rew)
cpd_3_2_rew = re._CPD(X_3_rew, firing_rates_2_inf_rew)
cpd_1_2_error = re._CPD(X_1_error, firing_rates_2_inf_error)
cpd_1_3_error = re._CPD(X_1_error, firing_rates_3_inf_error)
cpd_2_1_error = re._CPD(X_2_error, firing_rates_1_inf_error)
cpd_2_3_error = re._CPD(X_2_error, firing_rates_3_inf_error)
cpd_3_1_error = re._CPD(X_3_error, firing_rates_1_inf_error)
cpd_3_2_error = re._CPD(X_3_error, firing_rates_2_inf_error)
cpd_rew = np.nanmean([
cpd_1_2_rew, cpd_1_3_rew, cpd_2_1_rew, cpd_2_3_rew, cpd_3_1_rew,
cpd_3_2_rew
], 0)
cpd_error = np.nanmean([
cpd_1_2_error, cpd_1_3_error, cpd_2_1_error, cpd_2_3_error,
cpd_3_1_error, cpd_3_2_error
], 0)
pal = sns.cubehelix_palette(8)
pal_c = sns.cubehelix_palette(8, start=2, rot=0, dark=0, light=.95)
if interactions == True:
sub = 2
else:
sub = 1
plt.figure()
plt.subplot(2, sub, 1)
plt.plot(cpd_rew[:, 0], color=pal[0], label='Pre Init Period')
plt.plot(cpd_rew[:, 1], color=pal[2], label='Init Period')
plt.plot(cpd_rew[:, 2], color=pal[4], label='Choice Period')
plt.plot(cpd_rew[:, 3], color=pal[6], label='Reward Period')
plt.title(area + 'Between Tasks Reward Runs')
plt.legend()
sns.despine()
# plt.ylim(0,0.18)
plt.subplot(2, sub, 2)
plt.plot(cpd_error[:, 0], color=pal_c[0], label='Pre Init Period')
plt.plot(cpd_error[:, 1], color=pal_c[2], label='Init Period')
plt.plot(cpd_error[:, 2], color=pal_c[4], label='Choice Period')
plt.plot(cpd_error[:, 3], color=pal_c[6], label='Reward Period')
plt.title(area + 'Between Tasks Error Runs')
# plt.ylim(0,0.06)
if interactions == True:
plt.subplot(2, sub, 3)
plt.plot(cpd_rew_int[:, 0], color=pal[0], label='Pre Init Period')
plt.plot(cpd_rew_int[:, 1], color=pal[2], label='Init Period')
plt.plot(cpd_rew_int[:, 2], color=pal[4], label='Choice Period')
plt.plot(cpd_rew_int[:, 3], color=pal[6], label='Reward Period')
plt.title(area + 'Between Tasks Reward Runs Interactions with Choice')
plt.legend()
sns.despine()
# plt.ylim(0,0.18)
plt.subplot(2, sub, 4)
plt.plot(cpd_error_int[:, 0], color=pal_c[0], label='Pre Init Period')
plt.plot(cpd_error_int[:, 1], color=pal_c[2], label='Init Period')
plt.plot(cpd_error_int[:, 2], color=pal_c[4], label='Choice Period')
plt.plot(cpd_error_int[:, 3], color=pal_c[6], label='Reward Period')
plt.title(area + 'Between Tasks Error Runs Interactions with Choice')
# plt.ylim(0,0.06)
plt.legend()
sns.despine()
cpd_rew_perm = []
cpd_error_perm = []
cpd_rew_int_perm = []
cpd_error_int_perm = []
for i, ii, in enumerate(C_3_perm):
C_1 = np.concatenate(C_1_perm[i], 1)
C_2 = np.concatenate(C_3_perm[i], 1)
C_3 = np.concatenate(C_2_perm[i], 1)
if interactions == True:
X_nan, firing_rates_1_inf_rew,firing_rates_2_inf_rew,firing_rates_3_inf_rew,firing_rates_1_inf_error,firing_rates_2_inf_error,\
firing_rates_3_inf_error,firing_rates_1_inf_rew_int,firing_rates_2_inf_rew_int,firing_rates_3_inf_rew_int,firing_rates_1_inf_error_int,\
firing_rates_2_inf_error_int,firing_rates_3_inf_error_int = find_coefficients(C_1,C_2,C_3,interactions = interactions, a = a)
X_1_rew = X_nan[:, :5]
X_1_rew_int = X_nan[:, 5:10]
X_1_error = X_nan[:, 10:15]
X_1_error_int = X_nan[:, 15:20]
X_2_rew = X_nan[:, 20:25]
X_2_rew_int = X_nan[:, 25:30]
X_2_error = X_nan[:, 30:35]
X_2_error_int = X_nan[:, 35:40]
X_3_rew = X_nan[:, 40:45]
X_3_rew_int = X_nan[:, 45:50]
X_3_error = X_nan[:, 50:55]
X_3_error_int = X_nan[:, 55:60]
cpd_1_2_rew = re._CPD(X_1_rew, firing_rates_2_inf_rew)
cpd_1_3_rew = re._CPD(X_1_rew, firing_rates_3_inf_rew)
cpd_2_1_rew = re._CPD(X_2_rew, firing_rates_1_inf_rew)
cpd_2_3_rew = re._CPD(X_2_rew, firing_rates_3_inf_rew)
cpd_3_1_rew = re._CPD(X_3_rew, firing_rates_1_inf_rew)
cpd_3_2_rew = re._CPD(X_3_rew, firing_rates_2_inf_rew)
cpd_1_2_error = re._CPD(X_1_error, firing_rates_2_inf_error)
cpd_1_3_error = re._CPD(X_1_error, firing_rates_3_inf_error)
cpd_2_1_error = re._CPD(X_2_error, firing_rates_1_inf_error)
cpd_2_3_error = re._CPD(X_2_error, firing_rates_3_inf_error)
cpd_3_1_error = re._CPD(X_3_error, firing_rates_1_inf_error)
cpd_3_2_error = re._CPD(X_3_error, firing_rates_2_inf_error)
cpd_1_2_rew_int = re._CPD(X_1_rew_int, firing_rates_2_inf_rew_int)
cpd_1_3_rew_int = re._CPD(X_1_rew_int, firing_rates_3_inf_rew_int)
cpd_2_1_rew_int = re._CPD(X_2_rew_int, firing_rates_1_inf_rew_int)
cpd_2_3_rew_int = re._CPD(X_2_rew_int, firing_rates_3_inf_rew_int)
cpd_3_1_rew_int = re._CPD(X_3_rew_int, firing_rates_1_inf_rew_int)
cpd_3_2_rew_int = re._CPD(X_3_rew_int, firing_rates_2_inf_rew_int)
cpd_1_2_error_int = re._CPD(X_1_error_int,
firing_rates_2_inf_error_int)
cpd_1_3_error_int = re._CPD(X_1_error_int,
firing_rates_3_inf_error_int)
cpd_2_1_error_int = re._CPD(X_2_error_int,
firing_rates_1_inf_error_int)
cpd_2_3_error_int = re._CPD(X_2_error_int,
firing_rates_3_inf_error_int)
cpd_3_1_error_int = re._CPD(X_3_error_int,
firing_rates_1_inf_error_int)
cpd_3_2_error_int = re._CPD(X_3_error_int,
firing_rates_2_inf_error_int)
cpd_rew_int_perm.append(
np.nanmean([
cpd_1_2_rew_int, cpd_1_3_rew_int, cpd_2_1_rew_int,
cpd_2_3_rew_int, cpd_3_1_rew_int, cpd_3_2_rew_int
], 0))
cpd_error_int_perm.append(
np.nanmean([
cpd_1_2_error_int, cpd_1_3_error_int, cpd_2_1_error_int,
cpd_2_3_error_int, cpd_3_1_error_int, cpd_3_2_error_int
], 0))
else:
X_nan, firing_rates_1_inf_rew,firing_rates_2_inf_rew,firing_rates_3_inf_rew,firing_rates_1_inf_error,firing_rates_2_inf_error,\
firing_rates_3_inf_error = find_coefficients(C_1,C_2,C_3,interactions = interactions, a = a)
X_1_rew = X_nan[:, :5]
X_1_error = X_nan[:, 5:10]
X_2_rew = X_nan[:, 10:15]
X_2_error = X_nan[:, 15:20]
X_3_rew = X_nan[:, 20:25]
X_3_error = X_nan[:, 25:30]
cpd_1_2_rew = re._CPD(X_1_rew, firing_rates_2_inf_rew)
cpd_1_3_rew = re._CPD(X_1_rew, firing_rates_3_inf_rew)
cpd_2_1_rew = re._CPD(X_2_rew, firing_rates_1_inf_rew)
cpd_2_3_rew = re._CPD(X_2_rew, firing_rates_3_inf_rew)
cpd_3_1_rew = re._CPD(X_3_rew, firing_rates_1_inf_rew)
cpd_3_2_rew = re._CPD(X_3_rew, firing_rates_2_inf_rew)
cpd_1_2_error = re._CPD(X_1_error, firing_rates_2_inf_error)
cpd_1_3_error = re._CPD(X_1_error, firing_rates_3_inf_error)
cpd_2_1_error = re._CPD(X_2_error, firing_rates_1_inf_error)
cpd_2_3_error = re._CPD(X_2_error, firing_rates_3_inf_error)
cpd_3_1_error = re._CPD(X_3_error, firing_rates_1_inf_error)
cpd_3_2_error = re._CPD(X_3_error, firing_rates_2_inf_error)
cpd_rew_perm.append(
np.nanmean([
cpd_1_2_rew, cpd_1_3_rew, cpd_2_1_rew, cpd_2_3_rew,
cpd_3_1_rew, cpd_3_2_rew
], 0))
cpd_error_perm.append(
np.nanmean([
cpd_1_2_error, cpd_1_3_error, cpd_2_1_error, cpd_2_3_error,
cpd_3_1_error, cpd_3_2_error
], 0))
cpd_rew_perm = np.max(np.percentile(cpd_rew_perm, 95, axis=0), 0)
cpd_error_perm = np.max(np.percentile(cpd_error_perm, 95, axis=0), 0)
plt.subplot(2, sub, 1)
plt.hlines(cpd_rew_perm[0],
xmin=0,
xmax=63,
color=pal[0],
label='Pre Init Period',
linestyle=':')
plt.hlines(cpd_rew_perm[1],
xmin=0,
xmax=63,
color=pal[2],
label='Init Period',
linestyle=':')
plt.hlines(cpd_rew_perm[2],
xmin=0,
xmax=63,
color=pal[4],
label='Choice Period',
linestyle=':')
plt.hlines(cpd_rew_perm[3],
xmin=0,
xmax=63,
color=pal[6],
label='Reward Period',
linestyle=':')
plt.legend()
sns.despine()
plt.subplot(2, sub, 2)
plt.hlines(cpd_error_perm[0],
xmin=0,
xmax=63,
color=pal_c[0],
label='Pre Init Period',
linestyle=':')
plt.hlines(cpd_error_perm[1],
xmin=0,
xmax=63,
color=pal_c[2],
label='Init Period',
linestyle=':')
plt.hlines(cpd_error_perm[2],
xmin=0,
xmax=63,
color=pal_c[4],
label='Choice Period',
linestyle=':')
plt.hlines(cpd_error_perm[3],
xmin=0,
xmax=63,
color=pal_c[6],
label='Reward Period',
linestyle=':')
plt.legend()
sns.despine()
if interactions == True:
cpd_rew_int_perm = np.max(np.percentile(cpd_rew_int_perm, 95, axis=0),
0)
cpd_error_int_perm = np.max(
np.percentile(cpd_error_int_perm, 95, axis=0), 0)
plt.subplot(2, sub, 3)
plt.hlines(cpd_rew_int_perm[0],
xmin=0,
xmax=63,
color=pal[0],
label='Pre Init Period',
linestyle=':')
plt.hlines(cpd_rew_int_perm[1],
xmin=0,
xmax=63,
color=pal[2],
label='Init Period',
linestyle=':')
plt.hlines(cpd_rew_int_perm[2],
xmin=0,
xmax=63,
color=pal[4],
label='Choice Period',
linestyle=':')
plt.hlines(cpd_rew_int_perm[3],
xmin=0,
xmax=63,
color=pal[6],
label='Reward Period',
linestyle=':')
plt.legend()
sns.despine()
plt.subplot(2, sub, 4)
plt.hlines(cpd_error_int_perm[0],
xmin=0,
xmax=63,
color=pal_c[0],
label='Pre Init Period',
linestyle=':')
plt.hlines(cpd_error_int_perm[1],
xmin=0,
xmax=63,
color=pal_c[2],
label='Init Period',
linestyle=':')
plt.hlines(cpd_error_int_perm[2],
xmin=0,
xmax=63,
color=pal_c[4],
label='Choice Period',
linestyle=':')
plt.hlines(cpd_error_int_perm[3],
xmin=0,
xmax=63,
color=pal_c[6],
label='Reward Period',
linestyle=':')
plt.legend()
sns.despine()
def regression_RPE(data, perm=True):
C = []
cpd = []
dm = data['DM']
firing = data['Data']
if perm:
C_perm = [[] for i in range(perm)
] # To store permuted predictor loadings for each session.
cpd_perm = [[] for i in range(perm)
] # To store permuted cpd for each session.
for s, sess in enumerate(dm):
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1]
reward = DM[:, 2]
# state = DM[:,0]
rpe = DM[:, 14]
q1 = DM[:, 9]
q4 = DM[:, 10]
rand = np.random.normal(np.mean(q4), np.std(q4), len(q4))
ones = np.ones(len(rpe))
trials = len(ones)
predictors_all = OrderedDict([
('Reward', reward),
('Choice', choices),
#('State', state),
('RPE', rpe),
#('Q4', q4),
#('Q1', q1),
#('Noise', rand),
('ones', ones)
])
X = np.vstack(
predictors_all.values()).T[:len(choices), :].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
if perm:
for i in range(perm):
X_perm = np.roll(X, np.random.randint(trials), axis=0)
tstats = reg_f.regression_code(y, X_perm)
C_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm[i].append(
re._CPD(X_perm, y).reshape(n_neurons, n_timepoints,
n_predictors))
if perm: # Evaluate P values.
cpd_perm = np.stack(
[np.nanmean(np.concatenate(cpd_i, 0), 0) for cpd_i in cpd_perm], 0)
p = np.percentile(cpd_perm, 95, axis=0)
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
C = np.concatenate(C, 1)
return cpd_perm, p, cpd, C, predictors_all
def regression_time_choices_rewards_b_blocks_diff_tasks(data_HP, data_PFC,experiment_aligned_HP, experiment_aligned_PFC,start = 0, end = 20, HP = True):
C_1 = []
C_2 = []
C_3 = []
a_a_matrix_t_1_list, b_b_matrix_t_1_list,\
a_a_matrix_t_2_list, b_b_matrix_t_2_list,\
a_a_matrix_t_3_list, b_b_matrix_t_3_list,\
a_a_matrix_t_1_list_rewards, b_b_matrix_t_1_list_rewards,\
a_a_matrix_t_2_list_rewards, b_b_matrix_t_2_list_rewards,\
a_a_matrix_t_3_list_rewards, b_b_matrix_t_3_list_rewards,\
a_a_matrix_t_1_list_choices, b_b_matrix_t_1_list_choices,\
a_a_matrix_t_2_list_choices, b_b_matrix_t_2_list_choices,\
a_a_matrix_t_3_list_choices, b_b_matrix_t_3_list_choices = ch_rew_align.hieararchies_extract_rewards_choices(data_HP, data_PFC,experiment_aligned_HP, experiment_aligned_PFC,start = start, end = end, HP = HP)
for s, session in enumerate(b_b_matrix_t_1_list):
firing_rates_1 = b_b_matrix_t_1_list[s]
firing_rates_2 = b_b_matrix_t_2_list[s]
firing_rates_3 = b_b_matrix_t_3_list[s]
n_neurons = firing_rates_1.shape[0]
rewards_b_1 = b_b_matrix_t_1_list_rewards[s]
rewards_b_2 = b_b_matrix_t_2_list_rewards[s]
rewards_b_3 = b_b_matrix_t_3_list_rewards[s]
#rewards = np.hstack([rewards_a_1,rewards_a_2,rewards_a_3])
choices_b_1 = b_b_matrix_t_1_list_choices[s]
choices_b_2 = b_b_matrix_t_2_list_choices[s]
choices_b_3 = b_b_matrix_t_3_list_choices[s]
#choices = np.hstack([choices_a_1,choices_a_2,choices_a_3])
block_length = np.tile(np.arange(session.shape[1]/2),2)
# trial_number = np.tile(block_length,3)
ones_1 = np.ones(len(choices_b_1))
ones_2 = np.ones(len(choices_b_2))
ones_3 = np.ones(len(choices_b_3))
# Task 1
predictors = OrderedDict([('Reward', rewards_b_1),
('Choice', choices_b_1),
('Trial Number',block_length),
('Constant', ones_1)])
X = np.vstack(predictors.values()).T[:len(choices_b_1),:].astype(float)
n_predictors = X.shape[1]
y = firing_rates_1.reshape([len(firing_rates_1),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y.T, X)
C_1.append(tstats.reshape(n_predictors,n_neurons)) # Predictor loadings
# Task 2
predictors = OrderedDict([('Reward', rewards_b_2),
('Choice', choices_b_2),
('Trial Number',block_length),
('Constant', ones_2)])
X = np.vstack(predictors.values()).T[:len(choices_b_2),:].astype(float)
n_predictors = X.shape[1]
y = firing_rates_2.reshape([len(firing_rates_2),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y.T, X)
C_2.append(tstats.reshape(n_predictors,n_neurons)) # Predictor loadings
# Task 3
predictors = OrderedDict([('Reward', rewards_b_3),
('Choice', choices_b_3),
('Trial Number',block_length),
('Constant', ones_3)])
X = np.vstack(predictors.values()).T[:len(choices_b_3),:].astype(float)
n_predictors = X.shape[1]
y = firing_rates_3.reshape([len(firing_rates_3),-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y.T, X)
C_3.append(tstats.reshape(n_predictors,n_neurons)) # Predictor loadings
C_1 = np.concatenate(C_1,1)
C_2 = np.concatenate(C_2,1)
C_3 = np.concatenate(C_3,1)
return C_1,C_2,C_3
def crosscorr_weighted(all_sessions,HP, Data, DM, subj = 'm484'):
all_session_b1, all_session_a1, all_session_i1, all_session_b2, all_session_a2,\
all_session_i2, all_session_b3, all_session_a3, all_session_i3 = a_b_i_coding(Data,DM)
if subj == 'm484':
all_session_b1 = all_session_b1[:16]
all_session_a1 = all_session_a1[:16]
all_session_i1 = all_session_i1[:16]
all_session_b2 = all_session_b2[:16]
all_session_a2 = all_session_a2[:16]
all_session_i2 = all_session_i2[:16]
all_session_b3 = all_session_b3[:16]
all_session_a3 = all_session_a3[:16]
all_session_i3 = all_session_i3[:16]
elif subj == 'm479':
all_session_b1 = all_session_b1[16:24]
all_session_a1 = all_session_a1[16:24]
all_session_i1 = all_session_i1[16:24]
all_session_b2 = all_session_b2[16:24]
all_session_a2 = all_session_a2[16:24]
all_session_i2 = all_session_i2[16:24]
all_session_b3 = all_session_b3[16:24]
all_session_a3 = all_session_a3[16:24]
all_session_i3 = all_session_i3[16:24]
elif subj == 'm483':
all_session_b1 = all_session_b1[24:]
all_session_a1 = all_session_a1[24:]
all_session_i1 = all_session_i1[24:]
all_session_b2 = all_session_b2[24:]
all_session_a2 = all_session_a2[24:]
all_session_i2 = all_session_i2[24:]
all_session_b3 = all_session_b3[24:]
all_session_a3 = all_session_a3[24:]
all_session_i3 = all_session_i3[24:]
session_mean = []
for s,session in enumerate(all_sessions):
a1_ind, b1_ind,a2_ind, b2_ind,a3_ind, b3_ind, taskid, task = plot_tuning_curves(HP,subj,s)
all_session_b1_s = all_session_b1[s]
all_session_a1_s = all_session_a1[s]
all_session_i1_s = all_session_i1[s]
all_session_b2_s = all_session_b2[s]
all_session_a2_s = all_session_a2[s]
all_session_i2_s = all_session_i2[s]
all_session_b3_s = all_session_b3[s]
all_session_a3_s = all_session_a3[s]
all_session_i3_s = all_session_i3[s]
task_id_1 = task[(np.where(taskid == 1)[0])][0]
task_id_2 = task[(np.where(taskid == 2)[0])][0]
task_id_3 = task[(np.where(taskid == 3)[0])][0]
task = str(task_id_1) + '_' + str(task_id_2) + '_'+str(task_id_3)
colors = dict(mcolors.BASE_COLORS, **mcolors.CSS4_COLORS)
by_hsv = [*colors]
by_hsv = [color for color in by_hsv if 'dark' in color or 'medium' in color]
by_hsv = [color for color in by_hsv if not 'grey' in color]
fig = plt.figure()
for n in range(a1_ind.shape[1]):
fig.add_subplot(3,5, n+1)
plt.plot(np.mean(b2_ind[:,n,:], axis = 0),color=by_hsv[n], linestyle = '--', label = 'B2')
plt.plot(np.mean(b1_ind[:,n,:], axis = 0),color=by_hsv[n],linestyle = ':', label = 'B1')
plt.plot(np.mean(b3_ind[:,n,:], axis = 0),color=by_hsv[n],linestyle = '-.', label = 'B3')
plt.vlines(25, ymin = 0, ymax = np.max([np.mean(b2_ind[:,n,:], axis = 0),np.mean(b1_ind[:,n,:], axis = 0)]), color = 'grey', alpha = 0.5)
plt.vlines(36, ymin = 0, ymax = np.max([np.mean(b2_ind[:,n,:], axis = 0),np.mean(b1_ind[:,n,:], axis = 0)]), color = 'pink', alpha = 0.5)
plt.legend()
plt.title(s)
round_session = np.round(session)
x_max = 200
smooth_sd_ms = 0.5
bin_width_ms = 1
bin_edges_trial = np.arange(0,x_max, bin_width_ms)
hist_array = np.zeros((session.shape[0],session.shape[1],len(bin_edges_trial)-1))
ticks_label = []
for n,neuron in enumerate(round_session):
ticks_label.append(str(n+1))
for r,ripple in enumerate(neuron):
hist,edges = np.histogram(ripple, bins= bin_edges_trial)
smoothed = gaussian_filter1d(hist.astype(float), smooth_sd_ms)
hist_array[n,r,:] = smoothed
hist_mean = np.mean(hist_array, axis = 1)
figav = plt.figure()
for i,ii in enumerate(hist_mean):
figav.add_subplot(5,4,i+1)
plt.plot(ii, color = 'black')
combinations = list(itertools.combinations(range(hist_array.shape[0]), 2))
pos_1 = []
pos_2 = []
for i in combinations:
pos_1.append(i[0])
pos_2.append(i[1])
for i in combinations:
pos_1.append(i[1])
pos_2.append(i[0])
hist_array_cut = hist_array[:,:50,:]
c = []
corr_n_r = []
for i1,i2 in zip(pos_1,pos_2):
i = [i1,i2]
p = []
corr_n = []
for r,rr in zip(hist_array_cut[i1],hist_array_cut[i2]):
ripple = []
corr = []
correlation = np.correlate(r,rr, 'full')
for lag in range(1,50):
Design = np.ones((3,len(r)))
Design[1,:] = r
Design[2,:] = rr
model = LinearRegression().fit(Design[:,:-lag].T, rr[lag:])
corr.append(correlation[1])
ripple.append(model.coef_[1])
p.append(ripple)
corr_n.append(correlation)
if i == [1,0]:
plt.plot(np.mean(corr_n,axis = 0))
elif i == [0,1]:
plt.plot(np.mean(corr_n,axis = 0))
c.append(p)
corr_n_r.append(corr_n)
c = np.asarray(c)
mean_c = np.nanmean(c, axis = 1)
session_mean.append(mean_c)
BA = []
AB = []
AI = []
IA = []
BI = []
IB = []
BA_t2 = []
AB_t2 = []
AI_t2 = []
IA_t2 = []
BI_t2 = []
IB_t2 = []
BA_t3 = []
AB_t3 = []
AI_t3 = []
IA_t3 = []
BI_t3 = []
IB_t3 = []
for i1,i2 in zip(pos_1,pos_2):
BA.append(all_session_b1_s[i1]*all_session_a1_s[i2])
AB.append(all_session_a1_s[i1]*all_session_b1_s[i2])
AI.append(all_session_a1_s[i1]*all_session_i1_s[i2])
IA.append(all_session_i1_s[i1]*all_session_a1_s[i2])
BI.append(all_session_b1_s[i1]*all_session_i1_s[i2])
IB.append(all_session_i1_s[i1]*all_session_b1_s[i2])
BA_t2.append(all_session_b2_s[i1]*all_session_a2_s[i2])
AB_t2.append(all_session_a2_s[i1]*all_session_b2_s[i2])
AI_t2.append(all_session_a2_s[i1]*all_session_i2_s[i2])
IA_t2.append(all_session_i2_s[i1]*all_session_a2_s[i2])
BI_t2.append(all_session_b2_s[i1]*all_session_i2_s[i2])
IB_t2.append(all_session_i2_s[i1]*all_session_b2_s[i2])
BA_t3.append(all_session_b3[i1]*all_session_a3_s[i2])
AB_t3.append(all_session_a3[i1]*all_session_b3_s[i2])
AI_t3.append(all_session_a3[i1]*all_session_i3_s[i2])
IA_t3.append(all_session_i3[i1]*all_session_a3_s[i2])
BI_t3.append(all_session_b3[i1]*all_session_i3_s[i2])
IB_t3.append(all_session_i3[i1]*all_session_b3_s[i2])
Design_ports = np.asarray([np.ones(len(BA_t2)),BA_t2,AB_t2,AI_t2,IA_t2,BI_t2,IB_t2])
coefs = re.regression_code(mean_c,Design_ports.T)
plt.figure()
plt.plot(coefs[1], label = 'BA')
plt.plot(coefs[2], label = 'AB')
plt.plot(coefs[3], label = 'AI')
plt.plot(coefs[4], label = 'IA')
plt.plot(coefs[5], label = 'BI')
plt.plot(coefs[6], label = 'IB')
plt.legend()
def between_tasks(Data, DM, PFC=True):
cpd_true = []
C_true = []
cpd_aligned = []
C_aligned = []
C_sq_true = []
C_sq_aligned = []
if PFC == True:
ind_1 = np.arange(0, 26)
ind_2 = np.arange(1, 27)
ind_a = np.hstack((ind_1, ind_2))
ind_b = np.hstack((ind_2, ind_1))
else:
ind_1 = np.arange(0, 15)
ind_2 = np.arange(1, 16)
ind_a = np.hstack((ind_1, ind_2))
ind_b = np.hstack((ind_2, ind_1))
all_sessions_firing, all_session_dm = select_trials(Data, DM, 10)
for a, b in zip(ind_a, ind_b):
aligned_a, aligned_b, original_a, original_b, task_1_aligned = procrustes(
a, b, all_sessions_firing, all_session_dm)
target = np.transpose(task_1_aligned, [1, 0, 2])
source = np.transpose(original_a, [1, 0, 2])[40:80, :, :]
# Session 1 Task 2
dm_test = all_session_dm[a]
trials, n_neurons, n_timepoints = source.shape
reward_test = dm_test[:, 2][40:80]
state_test = dm_test[:, 0][40:80]
choices_test = dm_test[:, 1][40:80]
ones_test = np.ones(len(choices_test))
reward_choice = choices_test * reward_test
# Aligned Task 2 from Task 1
predictors_train = OrderedDict([('State', state_test),
('Reward', reward_test),
('Choice', choices_test),
('Reward Choice Int', reward_choice),
('ones', ones_test)])
X = np.vstack(predictors_train.values()).T[:trials, :].astype(float)
n_predictors = X.shape[1]
y = source.reshape(
[len(source),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_true.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
C_sq_true.append(
tstats.reshape(n_predictors, n_neurons, n_timepoints)**2)
cpd_true.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
# Aligned Using Neurons
n_predictors = X.shape[1]
y = target.reshape(
[len(target),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_aligned.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
C_sq_aligned.append(
tstats.reshape(n_predictors, n_neurons, n_timepoints)**2)
cpd_aligned.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
cpd_true = np.nanmean(np.concatenate(cpd_true, 0), axis=0)
C_sq_true = np.concatenate(C_sq_true, 1)
cpd_aligned = np.nanmean(np.concatenate(cpd_aligned, 0), axis=0)
C_sq_aligned = np.concatenate(C_sq_aligned, 1)
c = ['violet', 'black', 'green', 'blue', 'turquoise', 'grey', 'yellow', 'pink',\
'purple', 'darkblue', 'darkred', 'darkgreen','darkyellow','lightgreen']
p = [*predictors_train]
plt.figure()
for i in np.arange(cpd_true.shape[1] - 1):
plt.plot(cpd_true[:, i], label=p[i] + 'Real', color=c[i])
plt.plot(cpd_aligned[:, i],
label=p[i] + 'Aligned',
color=c[i],
linestyle='--')
plt.legend()
plt.ylabel('CPD')
plt.xlabel('Time in Trial')
plt.xticks([25, 35, 42], ['I', 'C', 'R'])
return cpd_aligned, cpd_true
def regression(Data, DM, PFC=True):
cpd_true = []
C_true = []
cpd_misaligned = []
C_misaligned = []
cpd_aligned = []
C_aligned = []
C_sq_true = []
C_sq_misaligned = []
C_sq_aligned = []
if PFC == True:
ind_1 = np.arange(0, 26)
ind_2 = np.arange(1, 27)
ind_a = np.hstack((ind_1, ind_2))
ind_b = np.hstack((ind_2, ind_1))
else:
ind_1 = np.arange(0, 15)
ind_2 = np.arange(1, 16)
ind_a = np.hstack((ind_1, ind_2))
ind_b = np.hstack((ind_2, ind_1))
misaligned_list = []
aligned_list = []
for a, b in zip(ind_a, ind_b):
all_sessions, all_session_dm, aligned_by_trial, original_a, original_b = in_progress(
a, b, Data, DM, misaligned_list, aligned_list)
# plt.figure()
# for i in np.arange(aligned_by_trial.shape[0]):
# plt.plot(np.mean(aligned_by_trial,1)[i,:])
# plt.figure()
# for i in np.arange(original_b.shape[0]):
# plt.plot(np.mean(original_b,1)[i,:])
#session_a = all_sessions[ind_a]
dm_test = all_session_dm[a]
session_training = np.transpose(original_a, [1, 0, 2])
session_misaligned = np.transpose(original_b, [1, 0, 2])
session_aligned = np.transpose(aligned_by_trial, [1, 0, 2])
trials, n_neurons, n_timepoints = session_training.shape
reward_test = dm_test[:, 2]
state_test = dm_test[:, 0]
choices_test = dm_test[:, 1]
ones_test = np.ones(len(choices_test))
trials_since_block = np.arange(0, 10)
trials_since_block = np.tile(trials_since_block, 12)
reward_choice = choices_test * reward_test
trial_sq = (np.asarray(trials_since_block) - 0.5)**2
choice_trials_sq = choices_test * trial_sq
interaction_trials_choice = trials_since_block * choices_test
# Original Using Neurons
predictors_train = OrderedDict([
('State', state_test),
('Reward', reward_test),
('Choice', choices_test),
#('Reward Choice Int', reward_choice),
#('Trials in Block', trials_since_block),
#('Squared Time in Block', trial_sq),
#('Trials x Choice', interaction_trials_choice),
#('Trials x Choice Sq',choice_trials_sq),
('ones', ones_test)
])
X = np.vstack(predictors_train.values()).T[:trials, :].astype(float)
n_predictors = X.shape[1]
y = session_training.reshape(
[len(session_training),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_true.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
C_sq_true.append(
tstats.reshape(n_predictors, n_neurons, n_timepoints)**2)
cpd_true.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
trials, n_neurons, n_timepoints = session_misaligned.shape
# Misaligned Using Neurons
y = session_misaligned.reshape(
[len(session_misaligned),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_misaligned.append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
C_sq_misaligned.append(
tstats.reshape(n_predictors, n_neurons, n_timepoints)**2)
cpd_misaligned.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
# Aligned Using Neurons
n_predictors = X.shape[1]
y = session_aligned.reshape(
[len(session_aligned),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C_aligned.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
C_sq_aligned.append(
tstats.reshape(n_predictors, n_neurons, n_timepoints)**2)
cpd_aligned.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
cpd_true = np.nanmean(np.concatenate(cpd_true, 0), axis=0)
C_true = np.concatenate(C_true, 1)
cpd_misaligned = np.nanmean(np.concatenate(cpd_misaligned, 0), axis=0)
C_misaligned = np.concatenate(C_misaligned, 1)
cpd_aligned = np.nanmean(np.concatenate(cpd_aligned, 0), axis=0)
C_aligned = np.concatenate(C_aligned, 1)
C_sq_true = np.concatenate(C_sq_true, 1)
C_sq_misaligned = np.concatenate(C_sq_misaligned, 1)
C_sq_aligned = np.concatenate(C_sq_aligned, 1)
C_sq_true[np.isfinite(C_sq_true) == False] = np.NaN
C_sq_true = np.nanmean(C_sq_true, 1)[:-1, :]
C_sq_misaligned = np.nanmean(C_sq_misaligned, 1)[:-1, :]
C_sq_aligned = np.nanmean(C_sq_aligned, 1)[:-1, :]
c = ['violet', 'black', 'green', 'blue', 'turquoise', 'grey', 'yellow', 'pink',\
'purple', 'darkblue', 'darkred', 'darkgreen','darkyellow','lightgreen']
p = [*predictors_train]
plt.figure()
for i in np.arange(C_sq_true.shape[0]):
plt.plot(C_sq_true[i, :], label=p[i] + 'Real', color=c[i])
plt.plot(C_sq_misaligned[i, :],
label=p[i] + 'Misaligned',
color=c[i],
linestyle='--')
plt.plot(C_sq_aligned[i, :],
label=p[i] + 'Aligned',
color=c[i],
linestyle=':')
plt.legend()
plt.ylabel('Coef Sq')
plt.xlabel('Time in Trial')
plt.xticks([25, 35, 42], ['I', 'C', 'R'])
cpd_true = cpd_true[:, :-1]
cpd_misaligned = cpd_misaligned[:, :-1]
cpd_aligned = cpd_aligned[:, :-1]
plt.figure()
for i in np.arange(cpd_true.shape[1]):
plt.plot(cpd_true[:, i], label=p[i] + 'Real', color=c[i])
plt.plot(cpd_misaligned[:, i],
label=p[i] + 'Misaligned',
color=c[i],
linestyle='--')
plt.plot(cpd_aligned[:, i],
label=p[i] + 'Aligned',
color=c[i],
linestyle=':')
plt.legend()
plt.ylabel('CPD')
plt.xlabel('Time in Trial')
plt.xticks([25, 35, 42], ['I', 'C', 'R'])
return misaligned_list, aligned_list
def regression_prev_choice(data, perm=True):
C = []
cpd = []
dm = data['DM'][0]
firing = data['Data'][0]
if perm:
C_perm = [[] for i in range(perm)
] # To store permuted predictor loadings for each session.
cpd_perm = [[] for i in range(perm)
] # To store permuted cpd for each session.
for s, sess in tqdm(enumerate(dm)):
DM = dm[s]
firing_rates = firing[s][1:, :, :]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1]
reward = DM[:, 2]
task = DM[:, 5]
task_id = np.where(np.diff(task))[0]
state = DM[:, 0]
stay = choices[0:-1] == choices[1:]
stay = stay * 1
stay = np.insert(stay, 0, 0)
lastreward = reward[0:-1]
lastreward = np.insert(lastreward, 0, 0)
rl = np.zeros(len(stay))
rl[0] = 1
rl_right = np.zeros(len(stay))
rl_right[0] = choices[0] == state[0]
choice_rr_start = -100
rl_wrong = np.zeros(len(stay))
rl_wrong[0] = choices[0] != state[0]
choice_rw_start = -100
for tr in range(len(stay)):
if tr > 0:
if stay[tr] == 1:
rl[tr] = rl[tr - 1] + 1
else:
rl[tr] = 1
if ((choices[tr] == choice_rr_start) &
(choices[tr] == state[tr])):
rl_right[tr] = rl_right[tr - 1] + 1
elif (choices[tr] == state[tr]):
rl_right[tr] = 1
choice_rr_start = choices[tr]
else:
rl_right[tr] = 0
choice_rr_start = -100
#If he made the wrong choice it can't be part of a correct run.
if ((choices[tr] == choice_rw_start) &
(choices[tr] != state[tr])):
rl_wrong[tr] = rl_wrong[tr - 1] + 1
elif choices[tr] != state[tr]:
rl_wrong[tr] = 1
choice_rw_start = choices[tr]
else:
rl_wrong[tr] = 0
choice_rw_start = -100 #If he made the right choice it can't be part of a wrong run.
trials = len(reward)
rl_wrong = rl_wrong[1:]
rl_right = rl_right[1:]
rl = rl[1:]
prev_choice = DM[:-1, 1]
choices = choices[1:]
reward = reward[1:]
task = task[1:]
state = state[1:]
ones = np.ones(len(reward))
int_repeat = choices * rl
int_repeat_corr = state * rl_right
int_repeat_incorr = state * rl_wrong
error_count = []
err_count = 0
for r, rew in enumerate(reward):
if rew == 0:
if reward[r] == reward[r - 1]:
err_count += 1
else:
err_count = 0
error_count.append(err_count)
predictors_all = OrderedDict([
('Reward', reward),
('Choice', choices),
('State', state),
('Previous Choice 1', prev_choice),
('Repeat', rl),
#('Error Count',error_count),
#('Repeat Incorrect', rl_wrong),
#('Repeat Correct', rl_right),
# ('Repeat Int', int_repeat),
#('Repeat Corr Int', int_repeat_corr),
#('Repeat Incorr Int', int_repeat_incorr),
('ones', ones)
])
X = np.vstack(
predictors_all.values()).T[:len(choices), :].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
if perm:
for i in range(perm):
X_perm = np.roll(X, np.random.randint(trials), axis=0)
tstats = reg_f.regression_code(y, X_perm)
C_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm[i].append(
re._CPD(X_perm, y).reshape(n_neurons, n_timepoints,
n_predictors))
if perm: # Evaluate P values.
cpd_perm = np.stack(
[np.nanmean(np.concatenate(cpd_i, 0), 0) for cpd_i in cpd_perm], 0)
p = np.percentile(cpd_perm, 95, axis=0)
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
C = np.concatenate(C, 1)
return cpd_perm, p, cpd, C, predictors_all
def regression_past_choice(data, perm=True):
C = []
cpd = []
dm = data['DM'][0]
firing = data['Data'][0]
if perm:
C_perm = [[] for i in range(perm)
] # To store permuted predictor loadings for each session.
cpd_perm = [[] for i in range(perm)
] # To store permuted cpd for each session.
for s, sess in tqdm(enumerate(dm)):
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
choices = DM[:, 1]
reward = DM[:, 2]
block = DM[:, 4]
block_df = np.diff(block)
task = DM[:, 5]
task_id = np.where(np.diff(task))[0]
ones = np.ones(len(block))
trials = len(ones)
stay = []
for c, ch in enumerate(choices):
if c > 0:
if choices[c - 1] == choices[c]:
stay.append(1)
else:
stay.append(0)
else:
stay.append(0)
a_side = 0
a_side_l = []
for r, rew in enumerate(reward):
if r in task_id:
a_side = 0
elif reward[r] == 1 and choices[r] == 1:
a_side += 1
a_side_l.append(a_side)
b_side = 0
b_side_l = []
for r, rew in enumerate(reward):
if r in task_id:
b_side = 0
elif reward[r] == 1 and choices[r] == 0:
b_side += 1
b_side_l.append(b_side)
stay_ch = np.asarray(stay) * choices
predictors_all = OrderedDict([('Reward', reward), ('Choice', choices),
('Stay', stay),
('Stay x Choice', stay_ch),
('Reward Cum A', a_side_l),
('Reward Cum B', b_side_l),
('ones', ones)])
X = np.vstack(
predictors_all.values()).T[:len(choices), :].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
if perm:
for i in range(perm):
X_perm = np.roll(X, np.random.randint(trials), axis=0)
tstats = reg_f.regression_code(y, X_perm)
C_perm[i].append(
tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_perm[i].append(
re._CPD(X_perm, y).reshape(n_neurons, n_timepoints,
n_predictors))
if perm: # Evaluate P values.
cpd_perm = np.stack(
[np.nanmean(np.concatenate(cpd_i, 0), 0) for cpd_i in cpd_perm], 0)
p = np.percentile(cpd_perm, 95, axis=0)
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
C = np.concatenate(C, 1)
return cpd_perm, p, cpd, C, predictors_all
def regression_general(data):
C = []
cpd = []
C_1 = []
C_2 = []
C_3 = []
cpd_1_2 = []
cpd_2_3 = []
dm = data['DM']
#dm = dm[:-1]
firing = data['Data']
#firing = firing[:-1]
for s, sess in enumerate(dm):
DM = dm[s]
firing_rates = firing[s]
n_trials, n_neurons, n_timepoints = firing_rates.shape
if n_neurons > 10:
session_trials_since_block = []
state = DM[:, 0]
choices = DM[:, 1]
reward = DM[:, 2]
b_pokes = DM[:, 7]
a_pokes = DM[:, 6]
task = DM[:, 5]
block = DM[:, 4]
block_df = np.diff(block)
taskid = rc.task_ind(task, a_pokes, b_pokes)
correct_choice = np.where(choices == state)[0]
correct = np.zeros(len(choices))
correct[correct_choice] = 1
a_since_block = []
trials_since_block = []
t = 0
#Bug in the state?
for st, s in enumerate(block):
if state[st - 1] != state[st]:
t = 0
else:
t += 1
trials_since_block.append(t)
session_trials_since_block.append(trials_since_block)
t = 0
for st, (s, c) in enumerate(zip(block, choices)):
if state[st - 1] != state[st]:
t = 0
a_since_block.append(t)
elif c == 1:
t += 1
a_since_block.append(t)
else:
a_since_block.append(0)
negative_reward_count = []
rew = 0
block_df = np.append(block_df, 0)
for r, b in zip(reward, block_df):
if r == 0:
rew += 1
negative_reward_count.append(rew)
elif r == 1:
rew -= 1
negative_reward_count.append(rew)
if b != 0:
rew = 0
positive_reward_count = []
rew = 0
block_df = np.append(block_df, 0)
for r, b in zip(reward, block_df):
if r == 1:
rew += 1
positive_reward_count.append(rew)
elif r == 0:
rew += 0
positive_reward_count.append(rew)
if b != 0:
rew = 0
positive_reward_count = np.asarray(positive_reward_count)
negative_reward_count = np.asarray(negative_reward_count)
choices_int = np.ones(len(reward))
choices_int[np.where(choices == 0)] = -1
reward_choice_int = choices_int * reward
interaction_trial_latent = trials_since_block * state
interaction_a_latent = a_since_block * state
int_a_reward = a_since_block * reward
interaction_trial_choice = trials_since_block * choices_int
reward_trial_in_block = trials_since_block * positive_reward_count
negative_reward_count_st = negative_reward_count * correct
positive_reward_count_st = positive_reward_count * correct
negative_reward_count_ch = negative_reward_count * choices
positive_reward_count_ch = positive_reward_count * choices
ones = np.ones(len(choices))
predictors_all = OrderedDict([
('Reward', reward),
('Choice', choices),
#('Correct', correct),
#('A in Block', a_since_block),
#('A in Block x Reward', int_a_reward),
('State', state),
('Trial in Block', trials_since_block),
#('Interaction State x Trial in Block', interaction_trial_latent),
#('Interaction State x A count', interaction_a_latent),
('Choice x Trials in Block', interaction_trial_choice),
('Reward x Choice', reward_choice_int),
# ('No Reward Count in a Block', negative_reward_count),
# ('No Reward x Correct', negative_reward_count_st),
# ('Reward Count in a Block', positive_reward_count),
# ('Reward Count x Correct', positive_reward_count_st),
# ('No reward Count x Choice',negative_reward_count_ch),
# ('Reward Count x Choice',positive_reward_count_ch),
# ('Reward x Trial in Block',reward_trial_in_block),
('ones', ones)
])
X = np.vstack(
predictors_all.values()).T[:len(choices), :].astype(float)
n_predictors = X.shape[1]
y = firing_rates.reshape(
[len(firing_rates),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y, X)
C.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd.append(
re._CPD(X, y).reshape(n_neurons, n_timepoints, n_predictors))
task_1 = np.where(taskid == 1)[0]
task_2 = np.where(taskid == 2)[0]
task_3 = np.where(taskid == 3)[0]
# Task 1
reward_t1 = reward[task_1]
choices_t1 = choices[task_1]
correct_t1 = correct[task_1]
a_since_block_t1 = np.asarray(a_since_block)[task_1]
int_a_reward_t1 = int_a_reward[task_1]
state_t1 = state[task_1]
trials_since_block_t1 = np.asarray(trials_since_block)[task_1]
interaction_trial_latent_t1 = interaction_trial_latent[task_1]
interaction_a_latent_t1 = interaction_a_latent[task_1]
interaction_trial_choice_t1 = interaction_trial_choice[task_1]
reward_choice_int_t1 = reward_choice_int[task_1]
negative_reward_count_t1 = negative_reward_count[task_1]
negative_reward_count_st_t1 = negative_reward_count_st[task_1]
positive_reward_count_t1 = positive_reward_count[task_1]
positive_reward_count_st_t1 = positive_reward_count_st[task_1]
negative_reward_count_ch_t1 = negative_reward_count_ch[task_1]
positive_reward_count_ch_t1 = positive_reward_count_ch[task_1]
reward_trial_in_block_t1 = reward_trial_in_block[task_1]
firing_rates_t1 = firing_rates[task_1]
ones = np.ones(len(choices_t1))
predictors = OrderedDict([
('Reward', reward_t1), ('Choice', choices_t1),
('Correct', correct_t1), ('A in Block', a_since_block_t1),
('A in Block x Reward', int_a_reward_t1), ('State', state_t1),
('Trial in Block', trials_since_block_t1),
('Interaction State x Trial in Block',
interaction_trial_latent_t1),
('Interaction State x A count', interaction_a_latent_t1),
('Choice x Trials in Block', interaction_trial_choice_t1),
('Reward x Choice', reward_choice_int_t1),
('No Reward Count in a Block', negative_reward_count_t1),
('No Reward x Correct', negative_reward_count_st_t1),
('Reward Count in a Block', positive_reward_count_t1),
('Reward Count x Correct', positive_reward_count_st_t1),
('No reward Count x Choice', negative_reward_count_ch_t1),
('Reward Count x Choice', positive_reward_count_ch_t1),
('Reward x Trial in Block', reward_trial_in_block_t1),
('ones', ones)
])
X_1 = np.vstack(
predictors.values()).T[:len(choices_t1), :].astype(float)
n_predictors = X_1.shape[1]
y_1 = firing_rates_t1.reshape(
[len(firing_rates_t1),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_1, X_1)
C_1.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
# Task 2
reward_t2 = reward[task_2]
choices_t2 = choices[task_2]
correct_t2 = correct[task_2]
a_since_block_t2 = np.asarray(a_since_block)[task_2]
int_a_reward_t2 = int_a_reward[task_2]
state_t2 = state[task_2]
trials_since_block_t2 = np.asarray(trials_since_block)[task_2]
interaction_trial_latent_t2 = interaction_trial_latent[task_2]
interaction_a_latent_t2 = interaction_a_latent[task_2]
interaction_trial_choice_t2 = interaction_trial_choice[task_2]
reward_choice_int_t2 = reward_choice_int[task_2]
negative_reward_count_t2 = negative_reward_count[task_2]
negative_reward_count_st_t2 = negative_reward_count_st[task_2]
positive_reward_count_t2 = positive_reward_count[task_2]
positive_reward_count_st_t2 = positive_reward_count_st[task_2]
negative_reward_count_ch_t2 = negative_reward_count_ch[task_2]
positive_reward_count_ch_t2 = positive_reward_count_ch[task_2]
reward_trial_in_block_t2 = reward_trial_in_block[task_2]
firing_rates_t2 = firing_rates[task_2]
ones = np.ones(len(choices_t2))
predictors = OrderedDict([
('Reward', reward_t2), ('Choice', choices_t2),
('Correct', correct_t2), ('A in Block', a_since_block_t2),
('A in Block x Reward', int_a_reward_t2), ('State', state_t2),
('Trial in Block', trials_since_block_t2),
('Interaction State x Trial in Block',
interaction_trial_latent_t2),
('Interaction State x A count', interaction_a_latent_t2),
('Choice x Trials in Block', interaction_trial_choice_t2),
('Reward x Choice', reward_choice_int_t2),
('No Reward Count in a Block', negative_reward_count_t2),
('No Reward x Correct', negative_reward_count_st_t2),
('Reward Count in a Block', positive_reward_count_t2),
('Reward Count x Correct', positive_reward_count_st_t2),
('No reward Count x Choice', negative_reward_count_ch_t2),
('Reward Count x Choice', positive_reward_count_ch_t2),
('Reward x Trial in Block', reward_trial_in_block_t2),
('ones', ones)
])
X_2 = np.vstack(
predictors.values()).T[:len(choices_t2), :].astype(float)
n_predictors = X_2.shape[1]
y_2 = firing_rates_t2.reshape(
[len(firing_rates_t2),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_2, X_2)
C_2.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
# Task 3
reward_t3 = reward[task_3]
choices_t3 = choices[task_3]
correct_t3 = correct[task_3]
a_since_block_t3 = np.asarray(a_since_block)[task_3]
int_a_reward_t3 = int_a_reward[task_3]
state_t3 = state[task_3]
trials_since_block_t3 = np.asarray(trials_since_block)[task_3]
interaction_trial_latent_t3 = interaction_trial_latent[task_3]
interaction_a_latent_t3 = interaction_a_latent[task_3]
interaction_trial_choice_t3 = interaction_trial_choice[task_3]
reward_choice_int_t3 = reward_choice_int[task_3]
negative_reward_count_t3 = negative_reward_count[task_3]
negative_reward_count_st_t3 = negative_reward_count_st[task_3]
positive_reward_count_t3 = positive_reward_count[task_3]
positive_reward_count_st_t3 = positive_reward_count_st[task_3]
negative_reward_count_ch_t3 = negative_reward_count_ch[task_3]
positive_reward_count_ch_t3 = positive_reward_count_ch[task_3]
reward_trial_in_block_t3 = reward_trial_in_block[task_3]
firing_rates_t3 = firing_rates[task_3]
ones = np.ones(len(choices_t3))
predictors = OrderedDict([
('Reward', reward_t3), ('Choice', choices_t3),
('Correct', correct_t3), ('A in Block', a_since_block_t3),
('A in Block x Reward', int_a_reward_t3), ('State', state_t3),
('Trial in Block', trials_since_block_t3),
('Interaction State x Trial in Block',
interaction_trial_latent_t3),
('Interaction State x A count', interaction_a_latent_t3),
('Choice x Trials in Block', interaction_trial_choice_t3),
('Reward x Choice', reward_choice_int_t3),
('No Reward Count in a Block', negative_reward_count_t3),
('No Reward x Correct', negative_reward_count_st_t3),
('Reward Count in a Block', positive_reward_count_t3),
('Reward Count x Correct', positive_reward_count_st_t3),
('No reward Count x Choice', negative_reward_count_ch_t3),
('Reward Count x Choice', positive_reward_count_ch_t3),
('Reward x Trial in Block', reward_trial_in_block_t3),
('ones', ones)
])
X_3 = np.vstack(
predictors.values()).T[:len(choices_t3), :].astype(float)
n_predictors = X_3.shape[1]
y_3 = firing_rates_t3.reshape(
[len(firing_rates_t3),
-1]) # Activity matrix [n_trials, n_neurons*n_timepoints]
tstats = reg_f.regression_code(y_3, X_3)
C_3.append(tstats.reshape(n_predictors, n_neurons,
n_timepoints)) # Predictor loadings
cpd_1_2.append(
_CPD_cross_task(X_1, X_2, y_1,
y_2).reshape(n_neurons, n_timepoints,
n_predictors))
cpd_2_3.append(
_CPD_cross_task(X_2, X_3, y_2,
y_3).reshape(n_neurons, n_timepoints,
n_predictors))
print(n_neurons)
cpd = np.nanmean(np.concatenate(cpd, 0), axis=0)
C = np.concatenate(C, 1)
C_1 = np.concatenate(C_1, 1)
C_2 = np.concatenate(C_2, 1)
C_3 = np.concatenate(C_3, 1)
cpd_1_2 = np.nanmean(np.concatenate(cpd_1_2, 0), axis=0)
cpd_2_3 = np.nanmean(np.concatenate(cpd_2_3, 0), axis=0)
return C, cpd, C_1, C_2, C_3, cpd_1_2, cpd_2_3, predictors_all, session_trials_since_block