def cp_als_test():
# Create synthetic dataset.
I, J, K, R = 25, 25, 25, 3 # dimensions and rank parameters
# Create a random tensor consisting of a low-rank component and noise.
X = tensortools.randn_ktensor((I, J, K), rank=R).full()
X += np.random.randn(I, J, K) # add some random noise
# Perform CP tensor decomposition.
U = tensortools.cp_als(X, rank=R, verbose=True)
V = tensortools.cp_als(X, rank=R, verbose=True)
# Compare the low-dimensional factors from the two fits.
fig, _, _ = tensortools.plot_factors(U.factors)
tensortools.plot_factors(V.factors, fig=fig)
# Align the two fits and print a similarity score.
similarity_score = tensortools.kruskal_align(U.factors,
V.factors,
permute_U=True,
permute_V=True)
print(similarity_score)
# Plot the results to see alignment.
fig, ax, po = tensortools.plot_factors(U.factors)
tensortools.plot_factors(V.factors, fig=fig)
plt.show()
def tca(X,
non_neg=True,
R=10,
prefix="",
max_iter=500,
epoc="all",
effect="all"):
# Fit CP tensor decomposition (two times).
U = None
V = None
opti_str = 'ncp_bcd_'
if non_neg:
U = tt.ncp_bcd(X, rank=R, verbose=True, max_iter=max_iter, tol=1e-6)
V = tt.ncp_bcd(X, rank=R, verbose=True, max_iter=max_iter, tol=1e-6)
else:
U = tt.cp_als(X, rank=R, verbose=True, max_iter=max_iter, tol=1e-6)
V = tt.cp_als(X, rank=R, verbose=True, max_iter=max_iter, tol=1e-6)
opti_str = 'cp_als_'
# Compare the low-dimensional factors from the two fits.
# fig, ax, po = tt.plot_factors(U.factors)
# tt.plot_factors(V.factors, fig=fig)
# fig.suptitle("raw models")
# fig.tight_layout()
# Align the two fits and print a similarity score.
sim = tt.kruskal_align(U.factors,
V.factors,
permute_U=True,
permute_V=True)
print(sim)
# Plot the results again to see alignment.
fig, ax, po = tt.plot_factors(U.factors,
plots=["scatter", "scatter", "line"])
tt.plot_factors(V.factors, plots=["scatter", "scatter", "line"], fig=fig)
[x.set_xticks([11.5, 15.5, 27.5, 31.5]) for x in ax[:, 2]]
ax[-1, 0].set_xlabel("SU #")
ax[-1, 1].set_xlabel("Trial #")
ax[-1, 2].set_xlabel("Time (s)")
ax[-1, 2].set_xticklabels(["S", "+1", "T", "+1"])
fig.suptitle("aligned models")
fig.tight_layout()
# Show plots.
plt.show()
fig.set_size_inches(40, 40)
fig.set_dpi(300)
fig.savefig(
opti_str + prefix + "tca_trial_" + epoc + "_" + effect + "_" +
str(X.shape[1]) + "_R" + str(R) + ".png",
dpi=300,
bbox_inches="tight",
)
return (U, V, sim)
def plotTCs(activity_tensor, targets, R, title=''):
U = tt.cp_als(activity_tensor, rank=R, verbose=False)
tt.plot_factors(U.factors, targets, plots=['scatter', 'line', 'bar'])
plt.title(title)
#plt.show()
# plt.savefig('tensorFactors.pdf')
#return neuron factors
return U.factors[2][:,0]
def run_tensor(f_behavior,
f_ephys,
smooth_method='both',
smooth_width=[80, 40],
pad=[400, 400],
z_score=True,
trial_duration=None,
max_duration=5000,
min_rate=0.1,
n_components=12,
epoch=None):
##get the data
X, trial_data = ptr.get_trial_spikes(f_behavior,
f_ephys,
smooth_method=smooth_method,
smooth_width=smooth_width,
pad=pad,
z_score=z_score,
trial_duration=trial_duration,
max_duration=max_duration,
min_rate=min_rate)
##reshape X to be neurons x timepoints x trials
X = X.transpose(1, 2, 0)
##take a specific window, if requested
if epoch == 'action':
if smooth_method == 'bins':
X = X[:, :int(pad[0] / smooth_width), :]
elif smooth_method == 'both':
X = X[:, :int(pad[0] / smooth_width[1]), :]
else:
X = X[:, :int(pad[0]), :]
if epoch == 'outcome':
if smooth_method == 'bins':
X = X[:, int(-pad[1] / smooth_width):, :]
elif smooth_method == 'both':
X = X[:, int(-pad[1] / smooth_width[1]):, :]
else:
X = X[:, int(-pad[1]):, :]
##now fit the model
model, info = tt.cp_als(X, n_components, nonneg=False, tol=1e-5)
print('Final reconstruction error : {}'.format(info['err_hist'][-1]))
return model, info, trial_data
for x in dir_list:
file_list = file_list + glob.glob(x + '/**/' + '*.h5',recursive=True)
file = 4
this_dir = file_list[file].split(sep='/')[-2]
data_dir = os.path.dirname(file_list[file])
data = ephys_data(data_dir = data_dir ,file_id = file, use_chosen_units = True)
data.firing_rate_params = dict(zip(['step_size','window_size','total_time','calc_type','baks_len'],
[25,250,7000,'conv',700]))
data.get_data()
data.get_firing_rates()
data.get_normalized_firing()
data.firing_overview('off')
all_firing_array = np.asarray(data.all_normal_off_firing)
#taste = 2
X = all_firing_array.swapaxes(1,2) #data.all_normal_off_firing[:,:,100:200].swapaxes(1,2) #
rank = 7
# Fit CP tensor decomposition (two times).
U = tt.cp_als(X, rank=rank, verbose=True)
# Compare the low-dimensional factors from the two fits.
fig, _, _ = tt.plot_factors(U.factors)
## We should be able to see differences in tastes by using distance matrices on trial factors
trial_factors = U.factors.factors[-1]
trial_distances = dist_mat(trial_factors,trial_factors)
plt.figure();plt.imshow(trial_distances)
def tensor_PCA(data):
n = 1
fig = plt.figure(1)
dm = data['DM']
data = data['Data']
predictors_correlated = []
for s, session in enumerate(data):
# Fit CP tensor decomposition (two times).
DM = dm[s]
R = 20
U = tt.cp_als(session, rank=R, verbose=True)
#V = tt.cp_als(session, rank=R, verbose=True)
# Compare the low-dimensional factors from the two fits.
#fig, ax, po = tt.plot_factors(U.factors)
#tt.plot_factors(V.factors, fig=fig)
#fig.suptitle("raw models")
#fig.tight_layout()
# Align the two fits and print a similarity score.
#sim = tt.kruskal_align(U.factors, V.factors, permute_U=True, permute_V=True)
#print(sim)
# Plot the results again to see alignment.
#fig, ax, po = tt.plot_factors(U.factors)
#tt.plot_factors(V.factors, fig=fig)
#fig.suptitle("aligned models")
#fig.tight_layout()
# Show plots.
#plt.show()
trial_factors = U.factors.factors[0]
state = DM[:, 0]
choices = DM[:, 1]
reward = DM[:, 2]
block = DM[:, 4]
block_df = np.diff(block)
correct_choice = np.where(choices == state)[0]
correct = np.zeros(len(choices))
correct[correct_choice] = 1
a_since_block = []
trials_since_block = []
t = 0
session_trials_since_block = []
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
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
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)
])
p = list(predictors_all.items())
for t in range(trial_factors.shape[1]):
for i in range(len(p)):
corr = np.corrcoef(trial_factors[:, t], p[i][1])
if abs(corr[1, 0]) > 0.65:
predictors_correlated.append(
(str(abs(corr[1, 0])) + ' ' + p[i][0]))
col = list(mcolors.CSS4_COLORS.keys())
col = np.asarray(col)
if 'x' in p[i][0]:
color = []
for ii, value in enumerate(p[i][1]):
value = np.int(value)
color.append(col[value])
else:
color_ind = np.asarray(np.where(p[i][1] == 0)[0])
color = np.asarray(
['green' for i in range(len(p[i][1]))])
color[color_ind] = 'black'
#fig.add_subplot(5,6,n)
#n +=1
#plt.scatter(np.arange(len(trial_factors[:,t])),trial_factors[:,t], c = color, s = 1,label=color)
#plt.title(p[i][0])
if 'x Trial' in p[i][0]:
plt.figure()
plt.scatter(np.arange(len(trial_factors[:, t])),
trial_factors[:, t],
c=color,
s=15,
label=color)
plt.vlines(np.where(block_df != 0)[0],
ymin=min(trial_factors[:, t]),
ymax=max(trial_factors[:, t]),
alpha=0.5)
x = trial_factors[:, t]
col_x = color
state_tial = p[i][1]
plt.title(p[i][0])
fig.tight_layout()
return predictors_correlated, x, col_x, state_tial
Created on Mon Jan 21 13:07:43 2019 @author: abuzarmahmood """ import tensortools as tt import numpy as np import matplotlib.pyplot as plt # Make synthetic dataset. I, J, K, R = 25, 25, 25, 4 # dimensions and rank X = tt.randn_ktensor((I, J, K), rank=R).full() X += np.random.randn(I, J, K) # add noise # Fit CP tensor decomposition (two times). U = tt.cp_als(X, rank=R, verbose=True) V = tt.cp_als(X, rank=R, verbose=True) # Compare the low-dimensional factors from the two fits. fig, _, _ = tt.plot_factors(U.factors) tt.plot_factors(V.factors, fig=fig) # Align the two fits and print a similarity score. sim = tt.kruskal_align(U.factors, V.factors, permute_U=True, permute_V=True) print(sim) # Plot the results again to see alignment. fig, ax, po = tt.plot_factors(U.factors) tt.plot_factors(V.factors, fig=fig) # Show plots.
this_dir + '/' + 'taste_' + str(taste)
if not os.path.exists(plot_dir):
os.makedirs(plot_dir)
this_off = all_firing_array[taste, :, :, :]
this_spikes = all_spikes_array[taste, :, :, :]
# =============================================================================
# total_off = this_off[0,:,:]
# for nrn in range(1,this_off.shape[0]):
# total_off = np.concatenate((total_off,this_off[int(nrn),:,:]),axis=1)
# =============================================================================
# Tensor decomposition for trial clustering
rank = 3 #X.shape[0]
U = tt.cp_als(np.swapaxes(this_off, 1, 2), rank=rank, verbose=True)
fig, ax, po = tt.plot_factors(U.factors)
[nrn_f, time_f, trial_f] = U.factors.factors
trial_dists = exposure.equalize_hist(dist_mat(trial_f, trial_f))
#trial_dists = exposure.equalize_hist(dist_mat(total_off,total_off))
# =============================================================================
# reduced_off_pca = pca(n_components = 15).fit(total_off)
# reduced_off = reduced_off_pca.transform(total_off)
# trial_dists_red = dist_mat(reduced_off,reduced_off)
# =============================================================================
clf = kmeans(n_clusters=n_components, n_init=200)
this_groups = clf.fit_predict(trial_dists)
# \_____|_|\__,_|___/\__\___|_| |_|_| |_|\__,_|_|___/ # # Clustering using tensor rank reduction firing_inds = range(80,160) lfp_inds = range(2000,4000) taste = 0 this_firing_data = np.rollaxis(firing_array[taste,:,:,firing_inds],0,3) # nrn x trial x time this_lfp_data = np.rollaxis(lfp_array[taste,:,lfp_inds],0,2) this_spike_data = np.rollaxis(spikes_array[taste,:,:,lfp_inds],0,3) rank = 7 # Fit CP tensor decomposition (two times). U = tt.cp_als(this_firing_data.swapaxes(1,2), rank=rank, verbose=False) # Compare the low-dimensional factors from the two fits. fig, _, _ = tt.plot_factors(U.factors) ## We should be able to see differences in tastes by using distance matrices on trial factors trial_factors = U.factors.factors[-1] trial_distances = exposure.equalize_hist(dist_mat(trial_factors,trial_factors)) plt.figure();plt.imshow(trial_distances) # Kmean clustering on trial factors n_components = 4 clf = kmeans(n_clusters = n_components, n_init = 500) this_groups = clf.fit_predict(trial_distances)
# =============================================================================
taste = 0
day3_data = day3_data[:, :, :, range(32)]
all_data = np.concatenate((day1_data, day3_data), axis=-1)
all_data_long = all_data[0, :, :, :]
for taste in range(1, all_data.shape[0]):
all_data_long = np.concatenate((all_data_long, all_data[taste, :, :, :]),
axis=-1)
# Fit CP tensor decomposition (two times).
rank = 10
repeats = 10
all_models = []
all_obj = []
for repeat in tqdm(range(repeats)):
U = tt.cp_als(all_data_long, rank=rank, verbose=False)
all_models.append(U)
all_obj.append(U.obj)
U = all_models[np.argmin(all_obj)]
## We should be able to see differences in tastes by using distance matrices on trial factors
trial_factors = U.factors.factors[-1]
trial_distances = dist_mat(trial_factors, trial_factors)
plt.figure()
plt.imshow(exposure.equalize_hist(trial_distances))
# pca on trial factors and plot by taste
trial_labels = np.sort([0, 1, 2, 3, 4, 5] * 32)
reduced_trials_pca = pca(n_components=2).fit_transform(trial_factors)
plt.scatter(reduced_trials_pca[:, 0], reduced_trials_pca[:, 1], c=trial_labels)
from utils import *
time_factor = np.load("data/time_factor.npy")
neuron_factor = np.load("data/neuron_factor.npy")
trial_factor = np.load("data/trial_factor.npy")
latent = np.load("data/latent.npy")
observed = np.load("data/observed.npy")
# Specify the tensor, and the rank (np. of factors)
X, rank = observed, 3
# Perform CP decompositon using TensorLy
factors_tl = parafac(X, rank=rank)
# Perform CP decomposition using tensortools
U = tt.cp_als(X, rank=rank, verbose=False)
factors_tt = U.factors.factors
# Reconstruct M, with the result of each library
M_tl = reconstruct(factors_tl)
M_tt = reconstruct(factors_tt)
# plot the decomposed factors
plot_factors(factors_tl)
plot_factors(factors_tt)
def decompose_three_way(tensor, rank, max_iter=501, verbose=False):
# a = np.random.random((rank, tensor.shape[0]))
b = np.random.random((rank, tensor.shape[1]))
c = np.random.random((rank, tensor.shape[2]))
import tensortools as tt import numpy as np # Make synthetic dataset. I, J, K, R = 25, 25, 25, 4 # dimensions and rank X = tt.randn_ktensor((I, J, K), rank=R).full() X += np.random.randn(I, J, K) # Fit CP tensor decomposition to first 20 trials. U = tt.cp_als(X[:, :, :20], rank=R, verbose=True) # Extend and re-initialize the factors along the final mode. Uext = U.factors.copy() Uext.factors[-1] = np.random.randn(K, R) Uext.shape = (I, J, K) # Fit model to the full dataset, only fitting the final set of factors. V = tt.cp_als(X, rank=R, init=Uext, skip_modes=[0, 1], verbose=True)