def train(cfg):
num_classes = int(cfg['n_classes'])
batch_size = int(cfg['batch_size'])
n_epochs = int(cfg['n_epochs'])
sample_size = int(cfg['fixed_size'])
cfg['loss'] = cfg['loss'].split(' ')
input_size = int(cfg['data_dim'])
#### DATA LOADING
trans_train = []
trans_val = []
if cfg['rnd_sampling']:
trans_train.append(ds.RndSampling(sample_size, maintain_prop=False))
trans_val.append(ds.RndSampling(sample_size, maintain_prop=False))
if cfg['standardization']:
trans_train.append(ds.SampleStandardization())
trans_val.append(ds.SampleStandardization())
#trans_train.append(T.Distance(norm=False))
#trans_val.append(T.Distance(norm=False))
if cfg['dataset'] == 'hcp20_graph':
dataset = ds.HCP20Dataset(
cfg['sub_list_train'],
cfg['dataset_dir'],
#k=4,
act=cfg['act'],
transform=transforms.Compose(trans_train),
#self_loops=T.AddSelfLoops(),
#distance=T.Distance(norm=True,cat=False),
return_edges=True,
load_one_full_subj=False)
elif cfg['dataset'] == 'left_ifof_ss_sl_graph':
dataset = ds.LeftIFOFSupersetGraphDataset(
cfg['sub_list_train'],
cfg['dataset_dir'],
transform=transforms.Compose(trans_train),
same_size=cfg['same_size'])
elif cfg['dataset'] == 'tractseg_500k':
dataset = ds.Tractseg500kDataset(
cfg['sub_list_train'],
cfg['dataset_dir'],
act=cfg['act'],
#fold_size=int(cfg['fold_size']),
transform=transforms.Compose(trans_train))
if 'graph' in cfg['dataset']:
DL = gDataLoader
else:
DL = DataLoader
dataloader = DL(dataset,
batch_size=batch_size,
shuffle=cfg['shuffling'],
num_workers=int(cfg['n_workers']),
pin_memory=True)
print("Dataset %s loaded, found %d samples" %
(cfg['dataset'], len(dataset)))
if cfg['val_in_train']:
if cfg['dataset'] == 'hcp20_graph':
val_dataset = ds.HCP20Dataset(
cfg['sub_list_val'],
cfg['val_dataset_dir'],
#k=4,
act=cfg['act'],
transform=transforms.Compose(trans_val),
#distance=T.Distance(norm=True,cat=False),
#self_loops=T.AddSelfLoops(),
return_edges=True,
load_one_full_subj=False)
elif cfg['dataset'] == 'tractseg_500k':
val_dataset = ds.Tractseg500kDataset(
cfg['sub_list_val'],
cfg['val_dataset_dir'],
act=cfg['act'],
#fold_size=int(cfg['fold_size']),
transform=transforms.Compose(trans_val))
elif cfg['dataset'] == 'left_ifof_ss_sl_graph':
val_dataset = ds.LeftIFOFSupersetGraphDataset(
cfg['sub_list_val'],
cfg['dataset_dir'],
transform=transforms.Compose(trans_val),
same_size=cfg['same_size'])
val_dataloader = DL(val_dataset,
batch_size=1,
shuffle=False,
num_workers=int(cfg['n_workers']),
pin_memory=True)
print("Validation dataset loaded, found %d samples" %
(len(val_dataset)))
# summary for tensorboard
if cfg['experiment_name'] != 'default':
for ext in range(100):
exp_name = cfg['experiment_name'] + '_%d' % ext
logdir = 'runs/%s' % exp_name
if not os.path.exists(logdir):
writer = SummaryWriter(logdir=logdir)
break
else:
writer = SummaryWriter()
tb_log_name = glob.glob('%s/events*' % logdir)[0].rsplit('/', 1)[1]
tb_log_dir = 'tb_logs/%s' % exp_name
os.system('mkdir -p %s' % tb_log_dir)
os.system('ln -sr %s/%s %s/%s ' %
(logdir, tb_log_name, tb_log_dir, tb_log_name))
os.system('cp main_dsl_config.py %s/config.txt' % (writer.logdir))
#### BUILD THE MODEL
classifier = get_model(cfg)
#### SET THE TRAINING
if cfg['optimizer'] == 'sgd_momentum':
optimizer = optim.SGD(classifier.parameters(),
lr=float(cfg['learning_rate']),
momentum=float(cfg['momentum']),
weight_decay=float(cfg['weight_decay']))
elif cfg['optimizer'] == 'adam':
optimizer = optim.Adam(classifier.parameters(),
lr=float(cfg['learning_rate']),
weight_decay=float(cfg['weight_decay']))
if cfg['lr_type'] == 'step':
lr_scheduler = optim.lr_scheduler.StepLR(optimizer,
int(cfg['lr_ep_step']),
gamma=float(cfg['lr_gamma']))
elif cfg['lr_type'] == 'plateau':
lr_scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer,
mode='min',
factor=float(cfg['lr_gamma']),
patience=int(cfg['patience']),
threshold=0.0001,
min_lr=float(cfg['min_lr']))
if cfg['loss'] == 'nll':
loss_fn = F.nll_loss
alfa = 0
cluster_loss_fn = None
classifier.cuda()
num_batch = len(dataset) / batch_size
print('num of batches per epoch: %d' % num_batch)
cfg['num_batch'] = num_batch
n_iter = 0
best_pred = 0
best_epoch = 0
current_lr = float(cfg['learning_rate'])
for epoch in range(n_epochs + 1):
# bn decay as in pointnet orig
if cfg['bn_decay'] and epoch % int(cfg['bn_decay_step']) == 0:
bn_momentum = float(cfg['bn_decay_init']) * float(
cfg['bn_decay_gamma'])**(epoch / int(cfg['bn_decay_step']))
bn_momentum = 1 - min(0.99, 1 - bn_momentum)
print('updated bn momentum to %f' % bn_momentum)
for module in classifier.modules():
if type(module) == torch.nn.BatchNorm1d:
module.momentum = bn_momentum
mean_acc, mean_prec, mean_iou, mean_recall, loss, n_iter = train_iter(
cfg, dataloader, classifier, optimizer, writer, epoch, n_iter,
cluster_loss_fn)
### validation during training
if epoch % int(cfg['val_freq']) == 0 and cfg['val_in_train']:
best_epoch, best_pred, loss_val = val_iter(cfg, val_dataloader,
classifier, writer,
epoch, cluster_loss_fn,
best_epoch, best_pred,
logdir)
if cfg['lr_type'] == 'step' and current_lr >= float(cfg['min_lr']):
lr_scheduler.step()
if cfg['lr_type'] == 'plateau':
lr_scheduler.step(loss_val)
for i, param_group in enumerate(optimizer.param_groups):
current_lr = float(param_group['lr'])
writer.add_scalar('train/lr', current_lr, epoch)
### logging
writer.add_scalar('train/epoch_acc',
torch.mean(mean_acc).item(), epoch)
writer.add_scalar('train/epoch_iou',
torch.mean(mean_iou).item(), epoch)
writer.add_scalar('train/epoch_prec',
torch.mean(mean_prec).item(), epoch)
writer.add_scalar('train/epoch_recall',
torch.mean(mean_recall).item(), epoch)
writer.close()
if best_epoch != n_epochs:
if cfg['save_model']:
modeldir = os.path.join(logdir, cfg['model_dir'])
torch.save(classifier.state_dict(),
'%s/model_ep-%d.pth' % (modeldir, epoch))
if cfg['save_pred']:
pred_dir = writer.logdir + '/predictions_%d' % epoch
if not os.path.exists(pred_dir):
os.makedirs(pred_dir)
for filename, value in pred_buffer.iteritems():
with open(os.path.join(pred_dir, filename) + '.pkl',
'wb') as f:
pickle.dump(value, f, protocol=pickle.HIGHEST_PROTOCOL)
if cfg['save_softmax_out']:
sm_dir = writer.logdir + '/sm_out_%d' % epoch
if not os.path.exists(sm_dir):
os.makedirs(sm_dir)
for filename, value in sm_buffer.iteritems():
with open(os.path.join(sm_dir, filename) + '_sm_1.pkl',
'wb') as f:
pickle.dump(value, f, protocol=pickle.HIGHEST_PROTOCOL)
for filename, value in sm2_buffer.iteritems():
with open(os.path.join(sm_dir, filename) + '_sm_2.pkl',
'wb') as f:
pickle.dump(value, f, protocol=pickle.HIGHEST_PROTOCOL)
if cfg['save_gf']:
gf_dir = writer.logdir + '/gf_%d' % epoch
if not os.path.exists(gf_dir):
os.makedirs(gf_dir)
i = 0
for filename, value in gf_buffer.iteritems():
if i == 3:
break
i += 1
with open(os.path.join(gf_dir, filename) + '.pkl', 'wb') as f:
pickle.dump(value, f, protocol=pickle.HIGHEST_PROTOCOL)
def train(cfg):
batch_size = int(cfg['batch_size'])
n_epochs = int(cfg['n_epochs'])
sample_size = int(cfg['fixed_size'])
cfg['loss'] = cfg['loss'].split(' ')
#### DATA LOADING
trans_train = []
trans_val = []
if cfg['rnd_sampling']:
trans_train.append(
ds.RndSampling(sample_size,
maintain_prop=False,
prop_vector=[1, 1]))
trans_val.append(ds.RndSampling(sample_size, maintain_prop=False))
dataset, dataloader = get_dataset(cfg, trans=trans_train)
val_dataset, val_dataloader = get_dataset(cfg, trans=trans_val, train=False)
# summary for tensorboard
writer = create_tb_logger(cfg)
dump_code(cfg, writer.logdir)
#### BUILD THE MODEL
classifier = get_model(cfg)
#### SET THE TRAINING
optimizer = get_optimizer(cfg, classifier)
lr_scheduler = get_lr_scheduler(cfg, optimizer)
classifier.cuda()
num_batch = len(dataset) / batch_size
print('num of batches per epoch: %d' % num_batch)
cfg['num_batch'] = num_batch
n_iter = 0
best_pred = 0
best_epoch = 0
current_lr = float(cfg['learning_rate'])
for epoch in range(n_epochs + 1):
# update bn decay
if cfg['bn_decay'] and epoch != 0 and epoch % int(
cfg['bn_decay_step']) == 0:
update_bn_decay(cfg, classifier, epoch)
loss, n_iter = train_ep(cfg, dataloader, classifier, optimizer, writer,
epoch, n_iter)
### validation during training
if epoch % int(cfg['val_freq']) == 0 and cfg['val_in_train']:
best_epoch, best_pred = val_ep(cfg, val_dataloader, classifier,
writer, epoch, best_epoch, best_pred)
# update lr
if cfg['lr_type'] == 'step' and current_lr >= float(cfg['min_lr']):
lr_scheduler.step()
if cfg['lr_type'] == 'plateau':
lr_scheduler.step(loss)
current_lr = get_lr(optimizer)
writer.add_scalar('train/lr', current_lr, epoch)
writer.close()