def test_train_MEG_swap():
dataset_path = ["Z:\Desktop\sub8\\ball1_sss.fif"]
dataset = MEG_Dataset(dataset_path, duration=1.0, overlap=0.0)
train_len, valid_len, test_len = len_split(len(dataset))
train_dataset, valid_dataset, test_dataset = random_split(
dataset, [train_len, valid_len, test_len]
)
device = "cpu"
trainloader = DataLoader(
train_dataset, batch_size=10, shuffle=False, num_workers=1
)
validloader = DataLoader(
valid_dataset, batch_size=2, shuffle=False, num_workers=1
)
epochs = 1
with torch.no_grad():
x, _, _ = iter(trainloader).next()
n_times = x.shape[-1]
net = models.MNet(n_times)
optimizer = SGD(net.parameters(), lr=0.0001, weight_decay=5e-4)
loss_function = torch.nn.MSELoss()
model, _, _ = train(
net,
trainloader,
validloader,
optimizer,
loss_function,
device,
epochs,
10,
0,
"",
)
print("Test succeeded!")
def test_ResNet_training():
train_set = TensorDataset(
torch.ones([50, 1, 204, 501]), torch.zeros([50, 2])
)
valid_set = TensorDataset(
torch.ones([10, 1, 204, 501]), torch.zeros([10, 2])
)
print(len(train_set))
device = "cpu"
trainloader = DataLoader(
train_set, batch_size=10, shuffle=False, num_workers=1
)
validloader = DataLoader(
valid_set, batch_size=2, shuffle=False, num_workers=1
)
epochs = 1
with torch.no_grad():
x, _ = iter(trainloader).next()
n_times = x.shape[-1]
net = models.ResNet([2, 2, 2], 64, n_times)
optimizer = Adam(net.parameters(), lr=0.0001)
loss_function = torch.nn.MSELoss()
model, _, _ = train(
net,
trainloader,
validloader,
optimizer,
loss_function,
device,
epochs,
10,
0,
"",
)
print("Test succeeded!")
def test_LeNet_train():
train_set = TensorDataset(
torch.ones([50, 1, 204, 501]), torch.zeros([50, 2])
)
valid_set = TensorDataset(
torch.ones([10, 1, 204, 501]), torch.zeros([10, 2])
)
print(len(train_set))
device = "cpu"
trainloader = DataLoader(
train_set, batch_size=10, shuffle=False, num_workers=1
)
validloader = DataLoader(
valid_set, batch_size=2, shuffle=False, num_workers=1
)
epochs = 1
# change between different network
net = models.LeNet5(501)
optimizer = Adam(net.parameters(), lr=0.00001)
loss_function = torch.nn.MSELoss()
print("begin training...")
model, _, _ = train(
net,
trainloader,
validloader,
optimizer,
loss_function,
device,
epochs,
10,
0,
"",
)
print("Training do not rise error")
def main(args):
data_dir = args.data_dir
figure_path = args.figure_dir
model_path = args.model_dir
file_name = "data.hdf5"
# Set skip_training to False if the model has to be trained, to True if the model has to be loaded.
skip_training = False
# Set the torch device
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print("Device = {}".format(device))
# Initialize parameters
parameters = Params_tunable(
subject_n=args.sub,
hand=args.hand,
batch_size=args.batch_size,
valid_batch_size=args.batch_size_valid,
test_batch_size=args.batch_size_test,
epochs=args.epochs,
lr=args.learning_rate,
duration=args.duration,
overlap=args.overlap,
patience=args.patience,
device=device,
y_measure=args.y_measure,
s_n_layer=args.s_n_layer,
s_kernel_size=args.s_kernel_size, # Local
# s_kernel_size=json.loads(' '.join(args.s_kernel_size)),
t_n_layer=args.t_n_layer,
t_kernel_size=args.t_kernel_size, # Local
# t_kernel_size=json.loads(' '.join(args.t_kernel_size)),
max_pooling=args.max_pooling,
ff_n_layer=args.ff_n_layer,
ff_hidden_channels=args.ff_hidden_channels,
dropout=args.dropout,
activation=args.activation,
desc=args.desc,
)
# Import data and generate train-, valid- and test-set
# Set if generate with RPS values or not (check network architecture used later)
print("Testing: {} ".format(parameters.desc))
dataset = MEG_Cross_Dataset_no_bp(
data_dir,
file_name,
parameters.subject_n,
mode="train",
y_measure=parameters.y_measure,
)
test_dataset = MEG_Cross_Dataset_no_bp(
data_dir,
file_name,
parameters.subject_n,
mode="test",
y_measure=parameters.y_measure,
)
# split the dataset in train, test and valid sets.
train_len, valid_len = len_split_cross(len(dataset))
# train_dataset, valid_test, test_dataset = random_split(dataset, [train_len, valid_len, test_len],
# generator=torch.Generator().manual_seed(42))
train_dataset, valid_dataset = random_split(dataset,
[train_len, valid_len])
print("Train dataset len {}, valid dataset len {}, test dataset len {}".
format(len(train_dataset), len(valid_dataset), len(test_dataset)))
# Initialize the dataloaders
trainloader = DataLoader(
train_dataset,
batch_size=parameters.batch_size,
shuffle=True,
num_workers=4,
)
validloader = DataLoader(
valid_dataset,
batch_size=parameters.valid_batch_size,
shuffle=True,
num_workers=4,
)
testloader = DataLoader(
test_dataset,
batch_size=parameters.test_batch_size,
shuffle=False,
num_workers=4,
)
# Initialize network
with torch.no_grad():
sample, y = iter(trainloader).next()
n_times = sample.shape[-1]
net = SCNN(
parameters.s_n_layer,
parameters.s_kernel_size,
parameters.t_n_layer,
parameters.t_kernel_size,
n_times,
parameters.ff_n_layer,
parameters.ff_hidden_channels,
parameters.dropout,
parameters.max_pooling,
parameters.activation,
)
print(net)
# Training loop or model loading
if not skip_training:
print("Begin training....")
# Check the optimizer before running (different from model to model)
optimizer = Adam(net.parameters(), lr=parameters.lr)
# optimizer = SGD(net.parameters(), lr=parameters.lr, weight_decay=5e-4)
scheduler = ReduceLROnPlateau(optimizer,
mode="min",
factor=0.5,
patience=15)
print("scheduler : ", scheduler)
loss_function = torch.nn.MSELoss()
start_time = timer.time()
net, train_loss, valid_loss = train(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
train_time = timer.time() - start_time
print("Training done in {:.4f}".format(train_time))
# visualize the loss as the network trained
fig = plt.figure(figsize=(10, 4))
plt.plot(range(1,
len(train_loss) + 1),
train_loss,
label="Training Loss")
plt.plot(range(1,
len(valid_loss) + 1),
valid_loss,
label="Validation Loss")
# find position of lowest validation loss
minposs = valid_loss.index(min(valid_loss)) + 1
plt.axvline(
minposs,
linestyle="--",
color="r",
label="Early Stopping Checkpoint",
)
plt.xlabel("epochs")
plt.ylabel("loss")
# plt.ylim(0, 0.5) # consistent scale
# plt.xlim(0, len(train_loss)+1) # consistent scale
plt.grid(True)
plt.legend()
plt.tight_layout()
plt.show()
image1 = fig
plt.savefig(os.path.join(figure_path, "loss_plot.pdf"))
if not skip_training:
# Save the trained model
save_pytorch_model(net, model_path, "model.pth")
else:
# Load the model (properly select the model architecture)
net = MNet()
net = load_pytorch_model(net, os.path.join(model_path, "model.pth"),
parameters.device)
# Evaluation
print("Evaluation...")
net.eval()
y_pred = []
y = []
y_pred_valid = []
y_valid = []
with torch.no_grad():
for data, labels in testloader:
data, labels = (
data.to(parameters.device),
labels.to(parameters.device),
)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(data))))
for data, labels in validloader:
data, labels = (
data.to(parameters.device),
labels.to(parameters.device),
)
y_valid.extend(list(labels[:, parameters.hand]))
y_pred_valid.extend((list(net(data))))
# Calculate Evaluation measures
print("Evaluation measures")
mse = mean_squared_error(y, y_pred)
rmse = mean_squared_error(y, y_pred, squared=False)
mae = mean_absolute_error(y, y_pred)
r2 = r2_score(y, y_pred)
print("mean squared error {}".format(mse))
print("root mean squared error {}".format(rmse))
print("mean absolute error {}".format(mae))
print("r2 score {}".format(r2))
# plot y_new against the true value focus on 100 timepoints
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
times = np.arange(200)
ax.plot(times, y_pred[0:200], color="b", label="Predicted")
ax.plot(times, y[0:200], color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("{}".format(parameters.y_measure))
ax.set_title("Sub {}, hand {}, {} prediction".format(
str(parameters.subject_n),
"sx" if parameters.hand == 0 else "dx",
parameters.y_measure,
))
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction_focus.pdf"))
plt.show()
# plot y_new against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
times = np.arange(len(y_pred))
ax.plot(times, y_pred, color="b", label="Predicted")
ax.plot(times, y, color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("{}".format(parameters.y_measure))
ax.set_title("Sub {}, hand {}, {} prediction".format(
str(parameters.subject_n),
"sx" if parameters.hand == 0 else "dx",
parameters.y_measure,
))
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction.pdf"))
plt.show()
# scatterplot y predicted against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
ax.scatter(np.array(y), np.array(y_pred), color="b", label="Predicted")
ax.set_xlabel("True")
ax.set_ylabel("Predicted")
# plt.legend()
plt.savefig(os.path.join(figure_path, "Scatter.pdf"))
plt.show()
# scatterplot y predicted against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
ax.scatter(np.array(y_valid),
np.array(y_pred_valid),
color="b",
label="Predicted")
ax.set_xlabel("True")
ax.set_ylabel("Predicted")
# plt.legend()
plt.savefig(os.path.join(figure_path, "Scatter_valid.pdf"))
plt.show()
# log the model and parameters using mlflow tracker
with mlflow.start_run(experiment_id=args.experiment) as run:
for key, value in vars(parameters).items():
mlflow.log_param(key, value)
mlflow.log_param("Time", train_time)
mlflow.log_metric("MSE", mse)
mlflow.log_metric("RMSE", rmse)
mlflow.log_metric("MAE", mae)
mlflow.log_metric("R2", r2)
mlflow.log_artifact(os.path.join(figure_path, "Times_prediction.pdf"))
mlflow.log_artifact(
os.path.join(figure_path, "Times_prediction_focus.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "loss_plot.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "Scatter.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "Scatter_valid.pdf"))
mlflow.pytorch.log_model(net, "models")
def main(args):
data_dir = args.data_dir
figure_path = args.figure_dir
model_path = args.model_dir
file_name = "ball_left_mean.npz"
# Set skip_training to False if the model has to be trained, to True if the model has to be loaded.
skip_training = False
# Set the torch device
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print("Device = {}".format(device))
# Initialize parameters
parameters = Params_cross(subject_n=args.sub,
hand=args.hand,
batch_size=args.batch_size,
valid_batch_size=args.batch_size_valid,
test_batch_size=args.batch_size_test,
epochs=args.epochs,
lr=args.learning_rate,
wd=args.weight_decay,
patience=args.patience,
device=device,
desc=args.desc)
# Set if generate with RPS values or not (check network architecture used later)
# if mlp = rps-mlp, elif rps = rps-mnet, else mnet
mlp = False
rps = True
print("Creating dataset")
# Generate the custom dataset
train_dataset = MEG_Within_Dataset_ivan(data_dir,
parameters.subject_n,
parameters.hand,
mode="train")
test_dataset = MEG_Within_Dataset_ivan(data_dir,
parameters.subject_n,
parameters.hand,
mode="test")
valid_dataset = MEG_Within_Dataset_ivan(data_dir,
parameters.subject_n,
parameters.hand,
mode="val")
# split the dataset in train, test and valid sets.
print("train set {}, val set {}, test set {}".format(
len(train_dataset), len(valid_dataset), len(test_dataset)))
# train_dataset, valid_test, test_dataset = random_split(dataset, [train_len, valid_len, test_len],
# generator=torch.Generator().manual_seed(42))
# train_dataset, valid_test, test_dataset = random_split(dataset, [train_len, valid_len, test_len])
# Better vizualization
# train_valid_dataset = Subset(dataset, list(range(train_len+valid_len)))
# test_dataset = Subset(dataset, list(range(train_len+valid_len, len(dataset))))
#
# train_dataset, valid_dataset = random_split(train_valid_dataset, [train_len, valid_len])
# Initialize the dataloaders
trainloader = DataLoader(train_dataset,
batch_size=parameters.batch_size,
shuffle=True,
num_workers=1)
validloader = DataLoader(valid_dataset,
batch_size=parameters.valid_batch_size,
shuffle=True,
num_workers=1)
testloader = DataLoader(test_dataset,
batch_size=parameters.test_batch_size,
shuffle=False,
num_workers=1)
# Get the n_times dimension
if mlp:
net = RPS_MLP()
# net = RPS_CNN()
else:
# Get the n_times dimension
with torch.no_grad():
sample, y, _ = iter(trainloader).next()
n_times = sample.shape[-1]
if rps:
net = RPS_MNet_ivan(n_times)
else:
net = MNet_ivan(n_times)
print(net)
total_params = 0
for name, parameter in net.named_parameters():
param = parameter.numel()
print("param {} : {}".format(name,
param if parameter.requires_grad else 0))
total_params += param
print(f"Total Trainable Params: {total_params}")
# Training loop or model loading
if not skip_training:
print("Begin training....")
# Check the optimizer before running (different from model to model)
# optimizer = Adam(net.parameters(), lr=parameters.lr)
optimizer = Adam(net.parameters(),
lr=parameters.lr,
weight_decay=parameters.wd)
# optimizer = SGD(net.parameters(), lr=parameters.lr, momentum=0.9, weight_decay=parameters.wd)
# optimizer = SGD(net.parameters(), lr=parameters.lr, momentum=0.9)
print("optimizer : ", optimizer)
scheduler = ReduceLROnPlateau(optimizer,
mode="min",
factor=0.5,
patience=15)
print("scheduler : ", scheduler)
loss_function = torch.nn.MSELoss()
# loss_function = torch.nn.L1Loss()
print("loss :", loss_function)
start_time = timer.time()
if mlp:
net, train_loss, valid_loss = train_bp_MLP(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
else:
if rps:
net, train_loss, valid_loss = train_bp(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
else:
net, train_loss, valid_loss = train(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
train_time = timer.time() - start_time
print("Training done in {:.4f}".format(train_time))
# visualize the loss as the network trained
fig = plt.figure(figsize=(10, 4))
plt.plot(range(1,
len(train_loss) + 1),
train_loss,
label='Training Loss')
plt.plot(range(1,
len(valid_loss) + 1),
valid_loss,
label='Validation Loss')
# find position of lowest validation loss
minposs = valid_loss.index(min(valid_loss)) + 1
plt.axvline(minposs,
linestyle='--',
color='r',
label='Early Stopping Checkpoint')
plt.xlabel("epochs")
plt.ylabel("loss")
# plt.ylim(0, 0.5) # consistent scale
# plt.xlim(0, len(train_loss)+1) # consistent scale
plt.grid(True)
plt.legend()
plt.tight_layout()
plt.show()
image1 = fig
plt.savefig(os.path.join(figure_path, "loss_plot.pdf"))
if not skip_training:
# Save the trained model
save_pytorch_model(net, model_path, "model.pth")
else:
# Load the model (properly select the model architecture)
net = RPS_MNet()
net = load_pytorch_model(net, os.path.join(model_path, "model.pth"),
parameters.device)
# Evaluation
print("Evaluation...")
net.eval()
y_pred = []
y = []
y_pred_valid = []
y_valid = []
# if RPS integration
with torch.no_grad():
if mlp:
for _, labels, bp in testloader:
labels, bp = labels.to(parameters.device), \
bp.to(parameters.device)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(bp))))
for _, labels, bp in validloader:
labels, bp = (
labels.to(parameters.device),
bp.to(parameters.device),
)
y_valid.extend(list(labels[:, parameters.hand]))
y_pred_valid.extend((list(net(bp))))
else:
if rps:
for data, labels, bp in testloader:
data, labels, bp = (
data.to(parameters.device),
labels.to(parameters.device),
bp.to(parameters.device),
)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(data, bp))))
for data, labels, bp in validloader:
data, labels, bp = (
data.to(parameters.device),
labels.to(parameters.device),
bp.to(parameters.device),
)
y_valid.extend(list(labels[:, parameters.hand]))
y_pred_valid.extend((list(net(data, bp))))
else:
for data, labels, _ in testloader:
data, labels = (
data.to(parameters.device),
labels.to(parameters.device),
)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(data))))
for data, labels, _ in validloader:
data, labels = (
data.to(parameters.device),
labels.to(parameters.device),
)
y_valid.extend(list(labels[:, parameters.hand]))
y_pred_valid.extend((list(net(data))))
# Calculate Evaluation measures
print("Evaluation measures")
mse = mean_squared_error(y, y_pred)
rmse = mean_squared_error(y, y_pred, squared=False)
mae = mean_absolute_error(y, y_pred)
r2 = r2_score(y, y_pred)
rmse_valid = mean_squared_error(y_valid, y_pred_valid, squared=False)
r2_valid = r2_score(y_valid, y_pred_valid)
valid_loss_last = min(valid_loss)
print("Test set ")
print("mean squared error {}".format(mse))
print("root mean squared error {}".format(rmse))
print("mean absolute error {}".format(mae))
print("r2 score {}".format(r2))
print("Validation set")
print("root mean squared error valid {}".format(rmse_valid))
print("r2 score valid {}".format(r2_valid))
print("last value of the validation loss: {}".format(valid_loss_last))
# plot y_new against the true value focus on 200 timepoints
fig, ax = plt.subplots(1, 1, figsize=[14, 6])
times = np.arange(1000)
ax.plot(times, y_pred[:1000], color="b", label="Predicted")
ax.plot(times, y[:1000], color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("Target")
ax.set_title("Sub {}, hand {} prediction".format(
str(parameters.subject_n), "sx" if parameters.hand == 0 else "dx"))
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction_focus.pdf"))
plt.show()
# plot y_new against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
times = np.arange(len(y_pred))
ax.plot(times, y_pred, color="b", label="Predicted")
ax.plot(times, y, color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("Target")
ax.set_title("Sub {}, hand {}, prediction".format(
str(parameters.subject_n), "sx" if parameters.hand == 0 else "dx"))
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction.pdf"))
plt.show()
# scatterplot y predicted against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
ax.scatter(np.array(y), np.array(y_pred), color="b", label="Predicted")
ax.set_xlabel("True")
ax.set_ylabel("Predicted")
# plt.legend()
plt.savefig(os.path.join(figure_path, "Scatter.pdf"))
plt.show()
# scatterplot y predicted against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
ax.scatter(np.array(y_valid),
np.array(y_pred_valid),
color="b",
label="Predicted")
ax.set_xlabel("True")
ax.set_ylabel("Predicted")
# plt.legend()
plt.savefig(os.path.join(figure_path, "Scatter_valid.pdf"))
plt.show()
# Save prediction for post analysis
out_file = "prediction_sub{}_hand_{}.npz".format(
str(parameters.subject_n), "left" if parameters.hand == 0 else "right")
np.savez(os.path.join(data_dir, out_file), y_pred=y_pred, y=y)
# log the model and parameters using mlflow tracker
with mlflow.start_run(experiment_id=args.experiment) as run:
for key, value in vars(parameters).items():
mlflow.log_param(key, value)
mlflow.log_param("Time", train_time)
mlflow.log_metric("MSE", mse)
mlflow.log_metric("RMSE", rmse)
mlflow.log_metric("MAE", mae)
mlflow.log_metric("R2", r2)
mlflow.log_metric("RMSE_Valid", rmse_valid)
mlflow.log_metric("R2_Valid", r2_valid)
mlflow.log_metric("Valid_loss", valid_loss_last)
mlflow.log_artifact(os.path.join(figure_path, "Times_prediction.pdf"))
mlflow.log_artifact(
os.path.join(figure_path, "Times_prediction_focus.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "loss_plot.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "Scatter.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "Scatter_valid.pdf"))
mlflow.pytorch.log_model(net, "models")
def main(args):
data_dir = args.data_dir
figure_path = args.figure_dir
model_path = args.model_dir
# Generate the data input path list. Each subject has 3 runs stored in 3 different files.
subj_id = "/sub" + str(args.sub) + "/ball0"
raw_fnames = [
"".join([data_dir, subj_id, str(i), "_sss_trans.fif"])
for i in range(1 if args.sub != 3 else 2, 4)
]
# local
# subj_id = "/sub"+str(args.sub)+"/ball"
# raw_fnames = ["".join([data_dir, subj_id, str(i), "_sss.fif"]) for i in range(1, 2)]
# Set skip_training to False if the model has to be trained, to True if the model has to be loaded.
skip_training = False
# Set the torch device
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print("Device = {}".format(device))
# Initialize parameters
parameters = Params_tunable(
subject_n=args.sub,
hand=args.hand,
batch_size=args.batch_size,
valid_batch_size=args.batch_size_valid,
test_batch_size=args.batch_size_test,
epochs=args.epochs,
lr=args.learning_rate,
duration=args.duration,
overlap=args.overlap,
patience=args.patience,
device=device,
y_measure=args.y_measure,
s_n_layer=args.s_n_layer,
# s_kernel_size=args.s_kernel_size, # Local
s_kernel_size=json.loads(" ".join(args.s_kernel_size)),
t_n_layer=args.t_n_layer,
# t_kernel_size=args.t_kernel_size, # Local
t_kernel_size=json.loads(" ".join(args.t_kernel_size)),
max_pooling=args.max_pooling,
ff_n_layer=args.ff_n_layer,
ff_hidden_channels=args.ff_hidden_channels,
dropout=args.dropout,
activation=args.activation,
)
# Set if generate with RPS values or not (check network architecture used later)
rps = True
# Generate the custom dataset
if rps:
dataset = MEG_Dataset(
raw_fnames,
parameters.duration,
parameters.overlap,
parameters.y_measure,
normalize_input=True,
)
else:
dataset = MEG_Dataset_no_bp(
raw_fnames,
parameters.duration,
parameters.overlap,
parameters.y_measure,
normalize_input=True,
)
# split the dataset in train, test and valid sets.
train_len, valid_len, test_len = len_split(len(dataset))
print(
"{} + {} + {} = {}?".format(
train_len, valid_len, test_len, len(dataset)
)
)
# train_dataset, valid_test, test_dataset = random_split(dataset, [train_len, valid_len, test_len],
# generator=torch.Generator().manual_seed(42))
train_dataset, valid_test, test_dataset = random_split(
dataset, [train_len, valid_len, test_len]
)
# Better vizualization
# train_valid_dataset = Subset(dataset, list(range(train_len+valid_len)))
# test_dataset = Subset(dataset, list(range(train_len+valid_len, len(dataset))))
#
# train_dataset, valid_dataset = random_split(train_valid_dataset, [train_len, valid_len])
# Initialize the dataloaders
trainloader = DataLoader(
train_dataset,
batch_size=parameters.batch_size,
shuffle=True,
num_workers=1,
)
validloader = DataLoader(
valid_test,
batch_size=parameters.valid_batch_size,
shuffle=True,
num_workers=1,
)
testloader = DataLoader(
test_dataset,
batch_size=parameters.test_batch_size,
shuffle=False,
num_workers=1,
)
# Get the n_times dimension
with torch.no_grad():
# Changes if RPS integration or not
if rps:
x, _, _ = iter(trainloader).next()
else:
x, _ = iter(trainloader).next()
n_times = x.shape[-1]
# Initialize network
# net = LeNet5(n_times)
# net = ResNet([2, 2, 2], 64, n_times)
# net = SCNN(parameters.s_n_layer,
# parameters.s_kernel_size,
# parameters.t_n_layer,
# parameters.t_kernel_size,
# n_times,
# parameters.ff_n_layer,
# parameters.ff_hidden_channels,
# parameters.dropout,
# parameters.max_pooling,
# parameters.activation)
# net = MNet(n_times)
# net = RPS_SCNN(parameters.s_n_layer,
# parameters.s_kernel_size,
# parameters.t_n_layer,
# parameters.t_kernel_size,
# n_times,
# parameters.ff_n_layer,
# parameters.ff_hidden_channels,
# parameters.dropout,
# parameters.max_pooling,
# parameters.activation)
net = RPS_MNet(n_times)
# net = RPS_MLP()
mlp = False
print(net)
# Training loop or model loading
if not skip_training:
print("Begin training....")
# Check the optimizer before running (different from model to model)
optimizer = Adam(net.parameters(), lr=parameters.lr, weight_decay=5e-4)
# optimizer = SGD(net.parameters(), lr=parameters.lr, weight_decay=5e-4)
scheduler = ReduceLROnPlateau(optimizer, mode="min", factor=0.5,
patience=15)
print("scheduler : ", scheduler)
loss_function = torch.nn.MSELoss()
start_time = timer.time()
if rps:
if mlp:
net, train_loss, valid_loss = train_bp_MLP(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
else:
net, train_loss, valid_loss = train_bp(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
else:
net, train_loss, valid_loss = train(
net,
trainloader,
validloader,
optimizer,
scheduler,
loss_function,
parameters.device,
parameters.epochs,
parameters.patience,
parameters.hand,
model_path,
)
train_time = timer.time() - start_time
print("Training done in {:.4f}".format(train_time))
# visualize the loss as the network trained
fig = plt.figure(figsize=(10, 4))
plt.plot(
range(1, len(train_loss) + 1), train_loss, label="Training Loss"
)
plt.plot(
range(1, len(valid_loss) + 1), valid_loss, label="Validation Loss"
)
# find position of lowest validation loss
minposs = valid_loss.index(min(valid_loss)) + 1
plt.axvline(
minposs,
linestyle="--",
color="r",
label="Early Stopping Checkpoint",
)
plt.xlabel("epochs")
plt.ylabel("loss")
# plt.ylim(0, 0.5) # consistent scale
# plt.xlim(0, len(train_loss)+1) # consistent scale
plt.grid(True)
plt.legend()
plt.tight_layout()
plt.show()
image1 = fig
plt.savefig(os.path.join(figure_path, "loss_plot.pdf"))
if not skip_training:
# Save the trained model
save_pytorch_model(net, model_path, "Baselinemodel_SCNN_swap.pth")
else:
# Load the model (properly select the model architecture)
net = RPS_MNet()
net = load_pytorch_model(
net, os.path.join(model_path, "model.pth"), parameters.device
)
# Evaluation
print("Evaluation...")
net.eval()
y_pred = []
y = []
# if RPS integration
with torch.no_grad():
if rps:
if mlp:
for _, labels, bp in testloader:
labels, bp = labels.to(parameters.device), bp.to(device)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(bp))))
else:
for data, labels, bp in testloader:
data, labels, bp = (
data.to(parameters.device),
labels.to(parameters.device),
bp.to(device),
)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(data, bp))))
else:
for data, labels in testloader:
data, labels = (
data.to(parameters.device),
labels.to(parameters.device),
)
y.extend(list(labels[:, parameters.hand]))
y_pred.extend((list(net(data))))
print("SCNN_swap...")
# Calculate Evaluation measures
mse = mean_squared_error(y, y_pred)
rmse = mean_squared_error(y, y_pred, squared=False)
mae = mean_absolute_error(y, y_pred)
r2 = r2_score(y, y_pred)
print("mean squared error {}".format(mse))
print("root mean squared error {}".format(rmse))
print("mean absolute error {}".format(mae))
print("r2 score {}".format(r2))
# plot y_new against the true value focus on 100 timepoints
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
times = np.arange(100)
ax.plot(times, y_pred[0:100], color="b", label="Predicted")
ax.plot(times, y[0:100], color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("{}".format(parameters.y_measure))
ax.set_title(
"Sub {}, hand {}, {} prediction".format(
str(parameters.subject_n),
"sx" if parameters.hand == 0 else "dx",
parameters.y_measure,
)
)
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction_focus.pdf"))
plt.show()
# plot y_new against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
times = np.arange(len(y_pred))
ax.plot(times, y_pred, color="b", label="Predicted")
ax.plot(times, y, color="r", label="True")
ax.set_xlabel("Times")
ax.set_ylabel("{}".format(parameters.y_measure))
ax.set_title(
"Sub {}, hand {}, {} prediction".format(
str(parameters.subject_n),
"sx" if parameters.hand == 0 else "dx",
parameters.y_measure,
)
)
plt.legend()
plt.savefig(os.path.join(figure_path, "Times_prediction.pdf"))
plt.show()
# scatterplot y predicted against the true value
fig, ax = plt.subplots(1, 1, figsize=[10, 4])
ax.scatter(np.array(y), np.array(y_pred), color="b", label="Predicted")
ax.set_xlabel("True")
ax.set_ylabel("Predicted")
# plt.legend()
plt.savefig(os.path.join(figure_path, "Scatter.pdf"))
plt.show()
# log the model and parameters using mlflow tracker
with mlflow.start_run(experiment_id=args.experiment) as run:
for key, value in vars(parameters).items():
mlflow.log_param(key, value)
mlflow.log_param("Time", train_time)
mlflow.log_metric("MSE", mse)
mlflow.log_metric("RMSE", rmse)
mlflow.log_metric("MAE", mae)
mlflow.log_metric("R2", r2)
mlflow.log_artifact(os.path.join(figure_path, "Times_prediction.pdf"))
mlflow.log_artifact(
os.path.join(figure_path, "Times_prediction_focus.pdf")
)
mlflow.log_artifact(os.path.join(figure_path, "loss_plot.pdf"))
mlflow.log_artifact(os.path.join(figure_path, "Scatter.pdf"))
mlflow.pytorch.log_model(net, "models")
def test_SCNN_training():
train_set = TensorDataset(
torch.ones([50, 1, 204, 501]), torch.zeros([50, 2])
)
valid_set = TensorDataset(
torch.ones([10, 1, 204, 501]), torch.zeros([10, 2])
)
print(len(train_set))
device = "cpu"
trainloader = DataLoader(
train_set, batch_size=10, shuffle=False, num_workers=1
)
validloader = DataLoader(
valid_set, batch_size=2, shuffle=False, num_workers=1
)
epochs = 1
n_spatial_layer = 2
spatial_kernel_size = [154, 51]
temporal_n_block = 1
# [[20, 10, 10, 8, 8, 5], [16, 8, 5, 5], [10, 10, 10, 10], [200, 200]]
temporal_kernel_size = [250]
max_pool = 2
mlp_n_layer = 3
mlp_hidden = 1024
mlp_dropout = 0.5
net = models.SCNN(
n_spatial_layer,
spatial_kernel_size,
temporal_n_block,
temporal_kernel_size,
501,
mlp_n_layer,
mlp_hidden,
mlp_dropout,
max_pool=max_pool,
)
optimizer = Adam(net.parameters(), lr=0.00001)
loss_function = torch.nn.MSELoss()
print("begin training...")
model, _, _ = train(
net,
trainloader,
validloader,
optimizer,
loss_function,
device,
epochs,
10,
0,
"",
)
print("Training do not rise error")