def run(params):
model = None
if 'load_model_from_dir' in params.__dict__ and params.load_model_from_dir:
print('Loading the model from an existing dir!')
model_params = pickle.load(
open(os.path.join(params.dir_name, 'config.pkl'), 'rb'))
if 'lookup_table' in params.__dict__:
model_params.lookup_table = params.lookup_table
if 'sentiment_dic' in params.__dict__:
model_params.sentiment_dic = params.sentiment_dic
model = models.setup(model_params)
model.load_state_dict(
torch.load(os.path.join(params.dir_name, 'model')))
model = model.to(params.device)
else:
model = models.setup(params).to(params.device)
if not ('fine_tune' in params.__dict__ and params.fine_tune == False):
print('Training the model!')
train(params, model)
model = torch.load(params.best_model_file)
os.remove(params.best_model_file)
performance_dict = test(model, params)
performance_str = print_performance(performance_dict, params)
save_model(model, params, performance_str)
return performance_dict
def train():
# Turn on training mode which enables dropout.
model.train()
total_loss = 0.
start_time = time.time()
ntokens = len(corpus.dictionary)
if args.model != 'Transformer':
hidden = model.init_hidden(args.batch_size)
for batch, i in enumerate(range(0, train_data.size(0) - 1, args.bptt)):
data, targets = get_batch(train_data, i)
# Starting each batch, we detach the hidden state from how it was previously produced.
# If we didn't, the model would try backpropagating all the way to start of the dataset.
model.zero_grad()
if args.model == 'Transformer':
output = model(data)
else:
hidden = repackage_hidden(hidden)
output, hidden = model(data, hidden)
loss = criterion(output.view(-1, ntokens), targets)
loss.backward()
# `clip_grad_norm` helps prevent the exploding gradient problem in RNNs / LSTMs.
torch.nn.utils.clip_grad_norm_(model.parameters(), args.clip)
for p in model.parameters():
p.data.add_(-lr, p.grad.data)
total_loss += loss.item()
if batch % args.log_interval == 0 and batch > 0:
cur_loss = total_loss / args.log_interval
elapsed = time.time() - start_time
print(
'| epoch {:3d} | {:5d}/{:5d} batches | lr {:02.2f} | ms/batch {:5.2f} | '
'loss {:5.2f} | ppl {:8.2f}'.format(
epoch, batch,
len(train_data) // args.bptt, lr,
elapsed * 1000 / args.log_interval, cur_loss,
math.exp(cur_loss)))
total_loss = 0
start_time = time.time()
import sys
from utils.model import train
DATASET_NAME = sys.argv[1]
if __name__ == '__main__':
train(DATASET_NAME)
def main(image_folder, model_folder, building_folder, figure_folder, info_csv,
stats_json_file, train_results, batch_size, ideal_batch_size, epochs,
device_name):
# Configure folders
image_folder = Path(image_folder)
model_folder = Path(model_folder)
building_folder = Path(building_folder)
stats_json_file = Path(stats_json_file)
figure_folder = Path(figure_folder)
# Seed program
torch.manual_seed(0)
# retrieve information on buildings
df = pd.read_csv(info_csv)
# Get information on a TIF
n_ch, h, w = get_tif_dims(list(image_folder.iterdir())[0])
# Get means and stds
if stats_json_file.exists():
mean_channels, std_channels = load_stats(stats_json_file)
else:
stats = compute_mean_std(image_folder, n_ch)
mean_channels = stats['mean']
std_channels = stats["std"]
with open(stats_json_file, 'w') as file:
json.dump(stats, file)
# New dims for image
pad_h, pad_w = 8 - h % 8, 8 - w % 8
# Prepare padding
if pad_h % 2 == 0:
top_p = bottom_p = pad_h // 2
else:
top_p, bottom_p = pad_h // 2, pad_h - (pad_h // 2)
if pad_w % 2 == 0:
left_p = right_p = pad_w // 2
else:
left_p, right_p = pad_w // 2, pad_w - (pad_w // 2)
img_pad = (left_p, top_p, right_p, bottom_p)
# Compose transforms
transforms = SemSegCompose(img_pad, mean_channels, std_channels, 360)
# Prepare loading function
# load_tif_with_mask = partial(
# load_tif,
# df=df,
# mean_vec=mean_channels,
# std_vec=std_channels,
# building_folder=building_folder,
# padding=(pad_h, pad_w))
# Make dataset
ds = MulPanSharpenDataset(image_folder,
building_folder,
df,
transforms=transforms)
# ds = datasets.DatasetFolder(root=image_folder,
# loader=load_tif_with_mask,
# extensions=('.tif',))
logger.info(f"N° of images: {len(ds)}")
logger.info(f"Type of img: {ds.label}")
train_ds, val_ds = split_dataset(ds, train_size=0.8)
logger.info(f"Train set size: {len(train_ds)}")
logger.info(f"Val set size: {len(val_ds)}")
train_dl = DataLoader(train_ds, batch_size=batch_size, shuffle=True)
val_dl = DataLoader(val_ds, batch_size=batch_size, shuffle=True)
logger.info(f"N° of iterations per batch (train): {len(train_dl)}")
logger.info(f"N° of iterations per batch (val): {len(val_dl)}")
# get model
logger.info("Getting U-Net model")
model = torch.hub.load('mateuszbuda/brain-segmentation-pytorch',
'unet',
in_channels=n_ch,
out_channels=2,
init_features=32,
pretrained=False)
device = torch.device(device_name)
logger.info(f"Mounting model on {device}")
model = model.to(device)
# Define criterion
logger.info("Defining cross-entropy loss with 11/89 ratio")
criterion = nn.CrossEntropyLoss(weight=torch.tensor([.11, .89]))
criterion = criterion.to(device)
# Define optimizer
logger.info("Defining Adam optimizer")
optimizer = optim.Adam(model.parameters(), lr=1e-3)
results = train(model, train_dl, val_dl, criterion, optimizer, epochs,
device, 2, model_folder, ideal_batch_size // batch_size)
# Saves model metrics as pickle file
with open(train_results, "wb") as f:
pickle.dump(results, f)
# Saves model
torch.save(model.state_dict(), model_folder / 'unet_model')
logger.info(f"Saved model at {model_folder / 'unet_model'}")
logging.info(f"Metrics evaluation. Check {figure_folder} for results.")
# Plot metrics
plot_loss(results, figure_folder)
logger.info("Loss curve created.")
plot_last_cm(results, figure_folder)
logger.info("Last confusion matrix created")
plot_correct_preds(results, figure_folder)
logger.info("Evolution of correct predictions created;")
plot_accuracy(results, figure_folder)
logger.info("Accuracy plot created.")
plot_iou(results, figure_folder)
logger.info("IoU evolution plot created.")
for i in range(5):
generate_masks(ds, model, figure_folder, i, 5)
logger.info("Created model results.")
# importing libraries
from sklearn.metrics import accuracy_score
from utils import read_dataset
from utils import model
# reading data
X_train, X_test, y_train, y_test = read_dataset.read_irisdata("../dataset/Iris.csv")
# number of K
k_value = 2
epoch = 5
'''
method : train()
arguments : number of clusters, features, labels, number of epochs
returns : k number of centroids
'''
centroids = model.train(k_value, X_train, y_train, epoch)
'''
method : predict()
arguments : number of clusters, k centroids, testing set
returns : predicted class label
'''
class_label = model.predict(k_value, centroids, X_test)
# accuracy score
accuracy = accuracy_score(y_test, class_label)
print('Test Accuracy: {}\n\n'.format(accuracy))
def run_nn(in_data_dir, index_file, out_path, run_dir, save_path_name='save', resume=None, batch_size=256, epochs=50, start_epoch=0, lr=1e-4, wd=1e-3, workers=12, no_cuda=True, seed=1):
# parser = argparse.ArgumentParser()
# parser.add_argument('path', default='/home/dell/eeg-data-sample/', type=str, help='path to the main dir of the experiment')
# parser.add_argument('--save', default='', type=str, metavar='PATH', help='save path under the main exp path')
# parser.add_argument('--resume', default='', type=str, metavar='PATH', help='path to a checkpoint (default: none)')
# parser.add_argument('--batch-size', type=int, default=256, help='input batch size for training (default: 512)')
# parser.add_argument('--epochs', type=int, default=50, help='number of epochs to train (default: 100)')
# parser.add_argument('--start-epoch', default=0, type=int, help='manual epoch number (useful on restarts)')
# parser.add_argument('--lr', type=float, default=1e-4, help='learning rate (default: 1e-4)')
# parser.add_argument('--wd', default=1e-3, type=float, help='weight decay (default: 1e-3)')
# parser.add_argument('--workers', type=int, default=12, help='number of data loading workers (default: 12)')
# parser.add_argument('--no-cuda', action='store_true', default=False, help='disables CUDA training')
# parser.add_argument('--seed', type=int, default=1, help='random seed (default: 1)')
# args = parser.parse_args()
# if args.save == '':
# args.save = os.path.join(os.path.dirname(args.path),
# '1DenseNet_sample_butter')
# else:
# args.save = os.path.join(os.path.dirname(args.path), args.save)
save_path = os.path.join('./Data/', run_dir, save_path_name)
torch.manual_seed(seed)
use_cuda = not no_cuda and torch.cuda.is_available()
cudnn.benchmark = True if use_cuda else False
print("===> Loading Datasets...")
print("\t===> Loading data index info")
with open(os.path.join('./Data/', index_file), "rb") as f:
data_splits = pickle.load(f)
print(len(data_splits['train']))
label_h5_path = os.path.join('./Data/', "labels.h5")
print(data_splits['train'][0])
print("\t===> Construct train set")
train_set = MontagePickleDataset(in_data_dir, list_index=data_splits['train'],
label_h5_path=label_h5_path, transform=None)
train_loader = DataLoader(dataset=train_set, batch_size=batch_size, shuffle=True, num_workers=workers)
print("\t===> Construct validation set")
val_set = MontagePickleDataset(in_data_dir, list_index=data_splits['validation'],
label_h5_path=label_h5_path, transform=None)
val_loader = DataLoader(dataset=val_set, batch_size=batch_size, shuffle=False, num_workers=workers)
print("===> Dataset loaded!")
# class_weights, pseudo_counts = compute_class_weight(data_splits['train'], alpha=0.2)
# pickle.dump(class_weights, open("/home/dell/eeg-data-sample/class_weights_random_sample_without_zero.pkl", "wb"),
# pickle.HIGHEST_PROTOCOL)
with open(os.path.join('./Data/', "class_weights.pkl"), "rb") as f:
class_weights = pickle.load(f)
class_weights = torch.from_numpy(class_weights).float()
print("===> Class Weights: {}".format(class_weights))
# Create model
print('===> Building a Model')
model = DenseNetClassifier()
if use_cuda:
model.cuda()
print('===> Model built!')
print('\t===> contains {} trainable params'.format(count_parameters(model)))
# print('\t===> DenseNet Final Features: {}'.format(model.features.num_features))
criterion = WeightedKLDivWithLogitsLoss(class_weights)
if use_cuda:
criterion.cuda()
optimizer = optim.Adam(model.parameters(), lr=lr, weight_decay=wd)
os.makedirs(save_path, exist_ok=True)
best_val_epoch = 0
best_val_loss = sys.float_info.max
best_val_acc = 0.0
train_losses, train_accuracies = [], []
val_losses, val_accuracies = [], []
# optionally resume from a checkpoint
if resume:
if os.path.isfile(resume):
print("===> Loading Checkpoint to Resume '{}'".format(resume))
checkpoint = torch.load(resume)
start_epoch = checkpoint['epoch'] + 1
best_val_epoch = checkpoint['best_epoch']
best_val_loss = checkpoint['best_valid_loss']
best_val_acc = checkpoint['best_valid_accuracy']
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
# scheduler.load_state_dict(checkpoint['scheduler'])
print("\t===> Loaded Checkpoint '{}' (epoch {})".format(resume, checkpoint['epoch']))
else:
raise FileNotFoundError("\t====> no checkpoint found at '{}'".format(resume))
start_time = timer()
writer = SummaryWriter()
for epoch in tqdm(range(start_epoch, epochs), desc="Epochs"):
# Training
train_loss, train_acc = train(model, train_loader, criterion, optimizer, use_cuda)
train_losses.append(train_loss)
train_accuracies.append(train_acc)
val_loss, val_acc = evaluate(model, val_loader, criterion, use_cuda)
val_losses.append(val_loss)
val_accuracies.append(val_acc)
print("train", train_loss, train_acc)
print("val", val_loss, val_acc)
# print("criterion", criterion)
writer.add_scalar('train_loss', train_loss, epoch)
writer.add_scalar('train_acc', train_acc, epoch)
writer.add_scalar('validation_loss', val_loss, epoch)
writer.add_scalar('validation_acc', val_acc, epoch)
# writer.add_scalar('learning_rate', lr, epoch)
is_best = val_loss < best_val_loss
# is_best = val_acc > best_val_acc
if is_best:
best_val_epoch = epoch
best_val_loss = val_loss
best_val_acc = val_acc
print("***IS BEST***")
with open(os.path.join(save_path, 'train_result.txt'), 'w') as f:
f.write('Best Validation Epoch: {}\n'.format(epoch))
f.write('Train Loss: {}\n'.format(train_loss))
f.write('Train Accuracy: {}\n'.format(train_acc))
f.write('Validation Loss: {}\n'.format(val_loss))
f.write('Validation Accuracy: {}\n'.format(val_acc))
torch.save(model, os.path.join(save_path, 'entire_model.pth'))
save_checkpoint({
'epoch': epoch,
'arch': str(model.__class__.__name__),
'state_dict': model.state_dict(),
'best_epoch': best_val_epoch,
'best_valid_loss': best_val_loss,
'best_valid_accuracy': best_val_acc,
'optimizer': optimizer.state_dict(),
# 'scheduler': scheduler.state_dict(),
}, is_best, filename=os.path.join(save_path, 'checkpoint.pth.tar'))
loss_curve, acc_curve = plot_learning_curves(train_losses, val_losses, train_accuracies, val_accuracies)
loss_curve.savefig(os.path.join(save_path, "loss.eps"), format='eps', bbox_inches='tight')
acc_curve.savefig(os.path.join(save_path, "acc.eps"), format='eps', bbox_inches='tight')
plt.close(loss_curve)
plt.close(acc_curve)
end_time = timer()
print("\nDone! - Elapsed Time: {} minutes".format((end_time - start_time) / 60))
writer.export_scalars_to_json("./all_scalars.json")
writer.close()
