def plot_lat_vs_time(data, individually=False):
tss = [s for id, s in data.iteritems()]
if individually:
for ts in tss:
plot_series(np.array(ts), 2, 1)
else:
plot_series(tss, 2, 1, variable_length=True)
def main(args):
# Device Configuration #
device = torch.device(
f'cuda:{args.gpu_num}' if torch.cuda.is_available() else 'cpu')
# Fix Seed for Reproducibility #
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
# Samples, Plots, Weights and CSV Path #
paths = [
args.samples_path, args.weights_path, args.csv_path,
args.inference_path
]
for path in paths:
make_dirs(path)
# Prepare Data #
data = pd.read_csv(args.data_path)[args.column]
# Prepare Data #
scaler_1 = StandardScaler()
scaler_2 = StandardScaler()
preprocessed_data = pre_processing(data, scaler_1, scaler_2, args.constant,
args.delta)
train_X, train_Y, test_X, test_Y = prepare_data(data, preprocessed_data,
args)
train_X = moving_windows(train_X, args.ts_dim)
train_Y = moving_windows(train_Y, args.ts_dim)
test_X = moving_windows(test_X, args.ts_dim)
test_Y = moving_windows(test_Y, args.ts_dim)
# Prepare Networks #
if args.model == 'conv':
D = ConvDiscriminator(args.ts_dim).to(device)
G = ConvGenerator(args.latent_dim, args.ts_dim).to(device)
elif args.model == 'lstm':
D = LSTMDiscriminator(args.ts_dim).to(device)
G = LSTMGenerator(args.latent_dim, args.ts_dim).to(device)
else:
raise NotImplementedError
#########
# Train #
#########
if args.mode == 'train':
# Loss Function #
if args.criterion == 'l2':
criterion = nn.MSELoss()
elif args.criterion == 'wgangp':
pass
else:
raise NotImplementedError
# Optimizers #
if args.optim == 'sgd':
D_optim = torch.optim.SGD(D.parameters(), lr=args.lr, momentum=0.9)
G_optim = torch.optim.SGD(G.parameters(), lr=args.lr, momentum=0.9)
elif args.optim == 'adam':
D_optim = torch.optim.Adam(D.parameters(),
lr=args.lr,
betas=(0., 0.9))
G_optim = torch.optim.Adam(G.parameters(),
lr=args.lr,
betas=(0., 0.9))
else:
raise NotImplementedError
D_optim_scheduler = get_lr_scheduler(D_optim, args)
G_optim_scheduler = get_lr_scheduler(G_optim, args)
# Lists #
D_losses, G_losses = list(), list()
# Train #
print(
"Training Time Series GAN started with total epoch of {}.".format(
args.num_epochs))
for epoch in range(args.num_epochs):
# Initialize Optimizers #
G_optim.zero_grad()
D_optim.zero_grad()
#######################
# Train Discriminator #
#######################
if args.criterion == 'l2':
n_critics = 1
elif args.criterion == 'wgangp':
n_critics = 5
for j in range(n_critics):
series, start_dates = get_samples(train_X, train_Y,
args.batch_size)
# Data Preparation #
series = series.to(device)
noise = torch.randn(args.batch_size, 1,
args.latent_dim).to(device)
# Adversarial Loss using Real Image #
prob_real = D(series.float())
if args.criterion == 'l2':
real_labels = torch.ones(prob_real.size()).to(device)
D_real_loss = criterion(prob_real, real_labels)
elif args.criterion == 'wgangp':
D_real_loss = -torch.mean(prob_real)
# Adversarial Loss using Fake Image #
fake_series = G(noise)
prob_fake = D(fake_series.detach())
if args.criterion == 'l2':
fake_labels = torch.zeros(prob_fake.size()).to(device)
D_fake_loss = criterion(prob_fake, fake_labels)
elif args.criterion == 'wgangp':
D_fake_loss = torch.mean(prob_fake)
D_gp_loss = args.lambda_gp * get_gradient_penalty(
D, series.float(), fake_series.float(), device)
# Calculate Total Discriminator Loss #
D_loss = D_fake_loss + D_real_loss
if args.criterion == 'wgangp':
D_loss += args.lambda_gp * D_gp_loss
# Back Propagation and Update #
D_loss.backward()
D_optim.step()
###################
# Train Generator #
###################
# Adversarial Loss #
fake_series = G(noise)
prob_fake = D(fake_series)
# Calculate Total Generator Loss #
if args.criterion == 'l2':
real_labels = torch.ones(prob_fake.size()).to(device)
G_loss = criterion(prob_fake, real_labels)
elif args.criterion == 'wgangp':
G_loss = -torch.mean(prob_fake)
# Back Propagation and Update #
G_loss.backward()
G_optim.step()
# Add items to Lists #
D_losses.append(D_loss.item())
G_losses.append(G_loss.item())
# Adjust Learning Rate #
D_optim_scheduler.step()
G_optim_scheduler.step()
# Print Statistics, Save Model Weights and Series #
if (epoch + 1) % args.log_every == 0:
# Print Statistics and Save Model #
print("Epochs [{}/{}] | D Loss {:.4f} | G Loss {:.4f}".format(
epoch + 1, args.num_epochs, np.average(D_losses),
np.average(G_losses)))
torch.save(
G.state_dict(),
os.path.join(
args.weights_path,
'TS_using{}_and_{}_Epoch_{}.pkl'.format(
G.__class__.__name__, args.criterion.upper(),
epoch + 1)))
# Generate Samples and Save Plots and CSVs #
series, fake_series = generate_fake_samples(
test_X, test_Y, G, scaler_1, scaler_2, args, device)
plot_series(series, fake_series, G, epoch, args,
args.samples_path)
make_csv(series, fake_series, G, epoch, args, args.csv_path)
########
# Test #
########
elif args.mode == 'test':
# Load Model Weights #
G.load_state_dict(
torch.load(
os.path.join(
args.weights_path, 'TS_using{}_and_{}_Epoch_{}.pkl'.format(
G.__class__.__name__, args.criterion.upper(),
args.num_epochs))))
# Lists #
real, fake = list(), list()
# Inference #
for idx in range(0, test_X.shape[0], args.ts_dim):
# Do not plot if the remaining data is less than time dimension #
end_ix = idx + args.ts_dim
if end_ix > len(test_X) - 1:
break
# Prepare Data #
test_data = test_X[idx, :]
test_data = np.expand_dims(test_data, axis=0)
test_data = np.expand_dims(test_data, axis=1)
test_data = torch.from_numpy(test_data).to(device)
start = test_Y[idx, 0]
noise = torch.randn(args.val_batch_size, 1,
args.latent_dim).to(device)
# Generate Fake Data #
with torch.no_grad():
fake_series = G(noise)
# Convert to Numpy format for Saving #
test_data = np.squeeze(test_data.cpu().data.numpy())
fake_series = np.squeeze(fake_series.cpu().data.numpy())
test_data = post_processing(test_data, start, scaler_1, scaler_2,
args.delta)
fake_series = post_processing(fake_series, start, scaler_1,
scaler_2, args.delta)
real += test_data.tolist()
fake += fake_series.tolist()
# Plot, Save to CSV file and Derive Metrics #
plot_series(real, fake, G, args.num_epochs - 1, args,
args.inference_path)
make_csv(real, fake, G, args.num_epochs - 1, args, args.inference_path)
derive_metrics(real, fake, args)
else:
raise NotImplementedError
def run_test(self):
SAMPLES_PER_CLASS = 50
N_CLASSES = 10
TIME = 150
BIN_SIZE = 10
DELAY = 50
DURATION = 10
SPARSITY = 0.05
CI_LVL = 0.95
# Determine the output and spatio-temporal response to various patterns, including unknown classes
for model in ["scratch", "trained"]:
if model == "trained": # Initially compute test statistics with model initialized from scratch, then do the same with trained model
try:
self.network: Net = load(self.config.RESULT_FOLDER +
"/model.pt")
except FileNotFoundError as e:
print("No saved network model found.")
raise e
# Direct network to GPU
if P.GPU: self.network.to_gpu()
self.stats_manager = utils.StatsManager(
self.network, self.config.CLASSES, self.config.ASSIGNMENTS)
self.network.train(False)
print("Testing " + model + " model...")
for type in ["out", "st"]:
if type == "out":
print("Computing output responses for various patterns")
else:
print(
"Computing spatio-temporal responses for various patterns"
)
unk = None
for k in range(N_CLASSES + 1):
pattern_name = str(k) if k < N_CLASSES else "rnd"
print("Pattern: " + pattern_name)
encoder = PoissonEncoder(
time=self.config.TIME, dt=self.config.DT
) if type == "out" else utils.CustomEncoder(
TIME, DELAY, DURATION, self.config.DT, SPARSITY)
dataset = self.data_manager.get_test(
[k], encoder,
SAMPLES_PER_CLASS) if k < N_CLASSES else None
# Get next input sample.
input_enc = next(
iter(dataset)
)["encoded_image"] if k < N_CLASSES else encoder(
torch.cat(
(torch.rand(SAMPLES_PER_CLASS, *
self.config.INPT_SHAPE) *
(self.config.INPT_NORM /
(.25 * self.config.INPT_SHAPE[1] *
self.config.INPT_SHAPE[2])
if self.config.INPT_NORM is not None else 1.),
torch.zeros(SAMPLES_PER_CLASS, *
self.config.LABEL_SHAPE)),
dim=3) * self.config.INTENSITY)
if P.GPU: input_enc = input_enc.cuda()
# Run the network on the input without labels
self.network.run(
inputs={"X": input_enc},
time=self.config.TIME if type == "out" else TIME)
# Update network activity monitoring
res = self.stats_manager.get_class_scores(
) if type == "out" else self.stats_manager.get_st_resp(
bin_size=BIN_SIZE)
if k not in self.config.CLASSES and k < N_CLASSES:
unk = res if unk is None else torch.cat(
(unk, res), dim=0)
# Reset network state
self.network.reset_state_variables()
# Save results
if type == "out":
mean = res.mean(dim=0)
std = res.std(dim=0)
count = res.size(0)
utils.plot_out_resp(
[mean], [std], [count], [pattern_name + " out"],
self.config.CLASSES, self.config.RESULT_FOLDER +
"/" + model + "/out_mean_" + pattern_name + ".png",
CI_LVL)
utils.plot_out_dist(
mean, std, self.config.CLASSES,
self.config.RESULT_FOLDER + "/" + model +
"/out_dist_" + pattern_name + ".png")
else:
utils.plot_st_resp(
[res.mean(dim=0)[:, :, [0, 3, 6, 9]]],
[pattern_name + " resp."], BIN_SIZE,
self.config.RESULT_FOLDER + "/" + model +
"/st_resp_" + pattern_name + ".png")
res = res.mean(dim=3).mean(dim=2)
utils.plot_series([res.mean(dim=0)], [res.std(dim=0)],
[pattern_name + " resp."], BIN_SIZE,
self.config.RESULT_FOLDER + "/" +
model + "/time_resp_" +
pattern_name + ".png", CI_LVL)
print("Pattern: unk")
if type == "out":
mean = unk.mean(dim=0)
std = unk.std(dim=0)
count = unk.size(0)
utils.plot_out_resp([mean], [std], [count], ["unk out"],
self.config.CLASSES,
self.config.RESULT_FOLDER + "/" +
model + "/out_mean_unk.png", CI_LVL)
utils.plot_out_dist(
mean, std, self.config.CLASSES,
self.config.RESULT_FOLDER + "/" + model +
"/out_dist_unk.png")
else:
utils.plot_st_resp([unk.mean(dim=0)[:, :, [0, 3, 6, 9]]],
["unk resp."], BIN_SIZE,
self.config.RESULT_FOLDER + "/" +
model + "/st_resp_unk.png")
unk = unk.mean(dim=3).mean(dim=2)
utils.plot_series([unk.mean(dim=0)], [unk.std(dim=0)],
["unk resp."], BIN_SIZE,
self.config.RESULT_FOLDER + "/" + model +
"/time_resp_unk.png", CI_LVL)
# Plot kernels
print("Plotting network kernels")
connections = {
"inpt": ("X", "Y"),
"exc": ("Y", "Y"),
"inh": ("Z", "Y")
}
lin_coord = self.network.coord_y_disc.view(
-1) * self.config.GRID_SHAPE[2] + self.network.coord_x_disc.view(
-1)
knl_idx = [
torch.nonzero(lin_coord == i)
for i in range(self.config.GRID_SHAPE[1] *
self.config.GRID_SHAPE[2])
]
knl_idx = [
knl_idx[i][0] if len(knl_idx[i]) > 0 else None
for i in range(len(knl_idx))
]
for name, conn in connections.items():
w = self.network.connections[conn].w.t()
lin_coord = lin_coord.to(w.device)
kernels = torch.zeros(self.config.GRID_SHAPE[1] *
self.config.GRID_SHAPE[2],
self.config.GRID_SHAPE[1],
self.config.GRID_SHAPE[2],
device=w.device)
if name != "inpt":
w = w.view(
self.config.NEURON_SHAPE[0] * self.config.NEURON_SHAPE[1],
self.config.NEURON_SHAPE[0] * self.config.NEURON_SHAPE[1])
w_red = torch.zeros(
self.config.NEURON_SHAPE[0] * self.config.NEURON_SHAPE[1],
self.config.GRID_SHAPE[1] * self.config.GRID_SHAPE[2],
device=w.device)
for i in range(w.size(1)):
w_red[:, lin_coord[i]] += w[:, i]
w = w_red
w = w.view(
self.config.NEURON_SHAPE[0] * self.config.NEURON_SHAPE[1],
self.config.GRID_SHAPE[1], self.config.GRID_SHAPE[2])
for i in range(kernels.size(0)):
if knl_idx[i] is not None:
kernels[i, :, :] = w[knl_idx[i], :, :]
utils.plot_grid(kernels,
path=self.config.RESULT_FOLDER + "/weights_" +
name + ".png",
num_rows=self.config.GRID_SHAPE[1],
num_cols=self.config.GRID_SHAPE[2])
# Calculate accuracy on test set
print("Evaluating test accuracy...")
self.eval_pass(self.tst_set, train=False)
print("Test accuracy: " +
str(100 * self.stats_manager.eval_accuracy[-1]) + "%")
print("Finished!")
window_size = 20
batch_size = 32
shuffle_buffer_size = 1000
# plot_series(time, series, title = "Original Data")
# plt.show()
print("\n Please be patient! _()_ This might take some time. \n")
# forecast = []
# for time in range(len(series) - window_size):
# forecast.append(model.predict(series[time:time + window_size][np.newaxis]))
# forecast = forecast[split_time-window_size:]
# results = np.array(forecast)[:, 0, 0]
rnn_forecast = model_forecast(model, series[..., np.newaxis], window_size)
rnn_forecast = rnn_forecast[split_time - window_size:-1, -1, 0]
plt.figure(figsize=(10, 6))
plot_series(time_valid, X_valid)
plot_series(
time_valid,
rnn_forecast,
title="conv_lstm prediction",
text="Conv1D(32)\nLSTM(32)\nLSTM(32)\nDense(1)\nloss = Huber\nOptimizer=SGD"
)
plt.show()
# plt.savefig('plotted_graphs/simple_model.png', bbox_inches='tight')
print()
# filter the individuals to get just those that have overlap in data points
# for at least NUM_YEARS years
filtered_indivs = max_subset(indivs, SECONDS_PER_YEAR * NUM_YEARS)
print('individuals with overlapping time series for at least %.f years' %
NUM_YEARS)
print(len(filtered_indivs))
# get the ids of the filtered individuals
ids = [i.id for i in filtered_indivs]
# get the time series of the filtered individuals
filtered_tss = [v for k, v in data.iteritems() if k in ids]
# interpolate for the filtered individual set
normd_tss = normalize_time_series(filtered_tss)
normd_tss = np.array(normd_tss)
print('shape of all time series after normalization')
print(normd_tss.shape)
print()
# plot lat vs time
plot_series(normd_tss, 2, 1)
# plot lat vs lon
plot_series(normd_tss)
normd_tss = normalize_time_series(tss, downsample_factor=args.ds_factor)
print('Shape of normalized data')
print(normd_tss.shape)
print()
# extract just the lat and lon coordinates since this is all we want to use for DTW
ptss = extract_lat_and_lon(normd_tss)
print('Shape of data without time')
print(ptss.shape)
print()
# instantiate a clusterer
print('Instantiating a clusterer')
clusterer = TsCluster(args.n_clusts, args.norm, stopping_threshold=args.st)
print('done')
print()
print('Clustering')
t0 = time()
clusterer.k_means_clust(ptss, 100, verbose=True)
dur = time() - t0
print('done in %fs' % dur)
print()
centroids = clusterer.get_centroids()
print('plotting centroids')
plot_series(centroids)
def run_bio_exp():
# For reproducibility
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
# Make inputs
regL = torch.zeros(1, *GRID_SHAPE)
regL[:, :, :, 0] = 1.
regL[:, :, -1, :] = 1.
upsL = torch.zeros(1, *GRID_SHAPE)
upsL[:, :, 0, :] = 1.
upsL[:, :, :, -1] = 1.
patterns = [regL, upsL]
ptn_names = ["regL", "upsL"]
try: # Try to load simulation results from file
results = torch.load(RESULTS_PATH + "/results.pt")
print("Found existing result file, results loaded")
except FileNotFoundError: # If file is not available, compute the results
results = {
"bef_tet":
torch.empty(NUM_ITERS,
len(patterns),
NUM_BINS,
GRID_SHAPE[1],
GRID_SHAPE[2],
device=DEVICE),
"aft_tet":
torch.empty(NUM_ITERS,
len(patterns),
NUM_BINS,
GRID_SHAPE[1],
GRID_SHAPE[2],
device=DEVICE)
}
for seed in range(NUM_ITERS):
print("#### CURRENT ITERATION: " + str(seed) + " ####")
torch.manual_seed(seed)
trn_encoder = PoissonEncoder(time=TIME, dt=DT)
tst_encoder = PoissonEncoder(
time=TIME,
dt=DT) if TST_ENCODER == ENC_POISSON else CustomEncoder(
time=TIME,
delay=DELAY,
duration=DURATION,
dt=DT,
sparsity=SPARSITY,
noise_intensity=NOISE_INTENSITY)
# Prepare network
print("Preparing networks")
net: Net = Net(inpt_shape=GRID_SHAPE,
neuron_shape=NEURON_SHAPE,
lbound=V_LB,
vrest=V_REST,
vreset=V_RESET,
vth=V_TH,
theta_w=THETA_W,
sigma=SIGMA,
conn_strength=CONN_STRENGTH,
sigma_lateral_exc=SIGMA_LATERAL_EXC,
exc_strength=EXC_STRENGTH,
sigma_lateral_inh=SIGMA_LATERAL_INH,
inh_strength=INH_STRENGTH,
dt=DT,
refrac=REFR,
tc_decay=V_DECAY,
tc_trace=TR_DECAY,
nu=LEARNING_RATE)
# Direct networks to GPU
if GPU: net = net.to_gpu()
# Test the network before tetanization
print("Testing network before tetanization")
results["bef_tet"][seed, :, :, :, :] = bio_test(
net, patterns, tst_encoder)
# Tetanize network on lower-L input
print("Tetanizing network")
bio_trn(net, regL, trn_encoder)
# Test the network after tetanization
print("Testing network after tetanization")
results["aft_tet"][seed, :, :, :, :] = bio_test(
net, patterns, tst_encoder)
print("Done\n")
print("Saving results")
os.makedirs(RESULTS_PATH, exist_ok=True)
torch.save(results, RESULTS_PATH + "/results.pt")
print("Saving plots")
bio_mean_series = {
"bef_tet":
torch.tensor([
[
0., 0., 0., 0., 0., 0.4, 0.5, 0.4, 0.3, 0.2, 0.1, 0.05, 0.05,
0.05, 0.05
], # pattern regL
[
0., 0., 0., 0., 0., 0.4, 0.6, 0.5, 0.3, 0.2, 0.1, 0.05, 0.05,
0.05, 0.05
] # pattern upsL
]),
"aft_tet":
torch.tensor([
[
0., 0., 0., 0., 0., 0.7, 1.1, 0.8, 0.6, 0.5, 0.4, 0.4, 0.3,
0.3, 0.2
], # pattern regL
[
0., 0., 0., 0., 0., 0.4, 0.5, 0.4, 0.2, 0.1, 0.1, 0.1, 0.1,
0.1, 0.1
] # pattern upsL
]),
}
bio_std_series = {
"bef_tet":
torch.tensor([
[
0., 0., 0., 0., 0., 0.1, 0.1, 0.1, 0.05, 0.05, 0.05, 0.05,
0.05, 0.05, 0.05
], # pattern regL
[
0., 0., 0., 0., 0., 0.1, 0.1, 0.1, 0.05, 0.05, 0.05, 0.05,
0.05, 0.05, 0.05
] # pattern upsL
]),
"aft_tet":
torch.tensor([
[
0., 0., 0., 0., 0., 0.15, 0.3, 0.2, 0.05, 0.15, 0.15, 0.15,
0.15, 0.15, 0.1
], # pattern regL
[
0., 0., 0., 0., 0., 0.1, 0.2, 0.1, 0.05, 0.05, 0.05, 0.05,
0.05, 0.05, 0.05
] # pattern upsL
]),
}
decay_time = {"bef_tet": 20., "aft_tet": 50.}
bio_mean = {
"bef_tet": torch.tensor([5.6, 4.7]),
"aft_tet": torch.tensor([6.4, 4.1])
}
bio_std = {
"bef_tet": torch.tensor([0.8, 0.8]),
"aft_tet": torch.tensor([0.7, 0.5])
}
bio_count = 4
bio_st_resp = {
"bef_tet":
torch.tensor([
[
[0.5, 0.2, 0.2, 0.2],
[0.5, 0., 0.5, 0.],
[0.2, 1., 0.2, 0.2],
[1., 0., 0., 0.],
[0., 1., 0.5, 0.],
[1., 0., 1., 0.2],
], # pattern regL
[
[0.2, 1., 1., 1.],
[0.5, 1., 0.2, 1.5],
[0.5, 0.2, 0.2, 0.5],
[0.5, 0.2, 0.5, 0.],
[0.2, 0.2, 0., 0.],
[0.2, 0., 0., 0.],
] # pattern upsL
]),
"aft_tet":
torch.tensor([
[
[1.8, 1., 0., 0.5],
[1.8, 1., 1.8, 0.],
[1., 1.8, 0., 0.5],
[1.8, 1., 0.1, 0.2],
[1., 1.8, 1., 1.],
[1.8, 0., 1.8, 0.5],
], # pattern regL
[
[0., 1., 1., 0.5],
[0.5, 0.5, 0., 1.],
[0.5, 0.5, 0.2, 0.2],
[0.2, 0.2, 0.5, 0.],
[0., 0.2, 0., 0.],
[0.2, 0., 0., 0.],
] # pattern upsL
]),
}
for k in results.keys():
out = None
for i in range(len(patterns)):
res = results[k][:, i, 0:OUT_BINS, :, :]
bio = bio_st_resp[k][i].unsqueeze(0) * torch.cat(
(torch.zeros(DELAY_BINS),
torch.exp(-torch.arange(OUT_BINS - DELAY_BINS) /
(TAU / BIN_SIZE))),
dim=0).view(-1, 1, 1)
utils.plot_st_resp([res[:, :, :, [0, 3, 6, 9]].mean(dim=0), bio],
["Simul.", "Biol."], BIN_SIZE, RESULTS_PATH +
"/" + k + "/st_resp_" + ptn_names[i] + ".png")
res = res.mean(dim=3).mean(dim=2)
utils.plot_series([res.mean(dim=0), bio_mean_series[k][i]],
[res.std(dim=0), bio_std_series[k][i]],
["Simul.", "Biol."], BIN_SIZE, RESULTS_PATH +
"/" + k + "/time_resp_" + ptn_names[i] + ".png",
CI_LVL)
bin_count = int(decay_time[k]) // BIN_SIZE
res = res[:, DELAY_BINS:DELAY_BINS + bin_count].mean(
dim=1, keepdim=True) * BIN_SIZE
out = res if out is None else torch.cat((out, res), dim=1)
mean = out.mean(dim=0)
std = out.std(dim=0)
count = out.size(0)
utils.plot_out_resp([mean, bio_mean[k]], [std, bio_std[k]],
[count, bio_count], ["Simul.", "Biol."], ptn_names,
RESULTS_PATH + "/" + k + "/out_mean.png", CI_LVL)
utils.plot_out_dist(mean, std, ptn_names,
RESULTS_PATH + "/" + k + "/out_dist_simul.png")
utils.plot_out_dist(bio_mean[k], bio_std[k], ptn_names,
RESULTS_PATH + "/" + k + "/out_dist_biol.png")
print("Finished")
import matplotlib.pyplot as plt from model import simple_model, lstm_model, conv_lstm from utils import windowed_dataset, plot_series, windowed_dataset1 from data_reader import load_data series, time = load_data() split_time = 3000 time_train = time[:split_time] X_train = series[:split_time] time_valid = time[split_time:] X_valid = series[split_time:] plot_series(time, series) plt.show() window_size = 30 batch_size = 32 shuffle_buffer_size = 1000 print(X_train.shape) dataset = windowed_dataset1(X_train, window_size, batch_size, shuffle_buffer_size) print(dataset) # IMPORT MODEL model = conv_lstm(window_size) lr_schedule = tf.keras.callbacks.LearningRateScheduler(lambda epoch: 1e-8 * 10 ** (epoch/20))
return errs
if __name__ == '__main__':
# get a map of individual id to all its data, ordered by time
indiv_to_ts = get_data_by_individual(args.fpath)
print('Number of individuals')
print(len(indiv_to_ts))
print()
if args.plot:
# let's plot out Irma's latitude against time
print('Plotting Irma\'s latitude over time')
plot_series(indiv_to_ts['Irma'], 2, 1)
print()
rdr = None
# optionally define a relative date range, e.g.
if args.rdr:
start = RelativeDate(args.rdr[0], args.rdr[1])
end = RelativeDate(args.rdr[2], args.rdr[3])
rdr = RelativeDateRange(start, end)
# get all the time series (splits)
tsos = get_time_series(indiv_to_ts, rdr, args.it)
print()
print('Total number of time series')
