def test_weights_scalar_handler_wrong_setup():
with pytest.raises(
TypeError,
match="Argument model should be of type torch.nn.Module"):
WeightsScalarHandler(None)
model = MagicMock(spec=torch.nn.Module)
with pytest.raises(TypeError,
match="Argument reduction should be callable"):
WeightsScalarHandler(model, reduction=123)
with pytest.raises(
TypeError,
match="Output of the reduction function should be a scalar"):
WeightsScalarHandler(model, reduction=lambda x: x)
wrapper = WeightsScalarHandler(model)
mock_logger = MagicMock()
mock_engine = MagicMock()
with pytest.raises(
RuntimeError,
match=
"Handler 'WeightsScalarHandler' works only with TensorboardLogger"
):
wrapper(mock_engine, mock_logger, Events.ITERATION_STARTED)
def test_weights_scalar_handler_frozen_layers(dummy_model_factory):
model = dummy_model_factory(with_grads=True, with_frozen_layer=True)
wrapper = WeightsScalarHandler(model)
mock_logger = MagicMock(spec=TensorboardLogger)
mock_logger.writer = MagicMock()
mock_engine = MagicMock()
mock_engine.state = State()
mock_engine.state.epoch = 5
wrapper(mock_engine, mock_logger, Events.EPOCH_STARTED)
mock_logger.writer.add_scalar.assert_has_calls([
call("weights_norm/fc2/weight", 12.0, 5),
call("weights_norm/fc2/bias", math.sqrt(12.0), 5)
],
any_order=True)
with pytest.raises(AssertionError):
mock_logger.writer.add_scalar.assert_has_calls(
[
call("weights_norm/fc1/weight", 12.0, 5),
call("weights_norm/fc1/bias", math.sqrt(12.0), 5)
],
any_order=True,
)
assert mock_logger.writer.add_scalar.call_count == 2
def test_weights_scalar_handler_wrong_setup():
model = MagicMock(spec=torch.nn.Module)
wrapper = WeightsScalarHandler(model)
mock_logger = MagicMock()
mock_engine = MagicMock()
with pytest.raises(RuntimeError, match="Handler 'WeightsScalarHandler' works only with TensorboardLogger"):
wrapper(mock_engine, mock_logger, Events.ITERATION_STARTED)
def custom_setup(self):
if self.tensorboard_logs:
tb_logger = TensorboardLogger(log_dir=self.tensorboard_logs)
tb_logger.attach(self.trainer,
log_handler=OutputHandler(
tag="training",
output_transform=lambda loss: {'loss': loss}),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(self.evaluator,
log_handler=OutputHandler(
tag="validation",
metric_names=["LossMetric"],
another_engine=self.trainer),
event_name=Events.EPOCH_COMPLETED)
if self.optional_tensorboard_features:
tb_logger.attach(self.trainer,
log_handler=OptimizerParamsHandler(
self.optimizer),
event_name=Events.ITERATION_STARTED)
tb_logger.attach(self.trainer,
log_handler=WeightsScalarHandler(self.model),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(self.trainer,
log_handler=WeightsHistHandler(self.model),
event_name=Events.EPOCH_COMPLETED)
tb_logger.attach(self.trainer,
log_handler=GradsScalarHandler(self.model),
event_name=Events.ITERATION_COMPLETED)
# This is important to close the tensorboard file logger
@self.trainer.on(Events.COMPLETED)
def end_tensorboard(trainer):
logger.info("Training completed")
tb_logger.close()
if self.embeddings_name:
@self.trainer.on(Events.COMPLETED)
def log_embeddings(trainer):
if hasattr(self.model, self.embeddings_name) and hasattr(
self.dataset_splits, "vectorizer") and TENSORBOARD:
logger.info(
f"Logging embeddings ({self.embeddings_name}) to Tensorboard!"
)
embeddings = getattr(self.model,
self.embeddings_name).weight.data
metadata = [
str(self.dataset_splits.vectorizer.data_vocab.
_id2token[token_index]).encode('utf-8')
for token_index in range(embeddings.shape[0])
]
self.writer.add_embedding(
mat=embeddings,
metadata=metadata,
global_step=self.trainer.state.epoch)
def test_weights_scalar_handler_whitelist(dummy_model_factory):
model = dummy_model_factory()
wrapper = WeightsScalarHandler(model, whitelist=["fc2.weight"])
mock_logger = MagicMock(spec=TensorboardLogger)
mock_logger.writer = MagicMock()
mock_engine = MagicMock()
mock_engine.state = State()
mock_engine.state.epoch = 5
wrapper(mock_engine, mock_logger, Events.EPOCH_STARTED)
mock_logger.writer.add_scalar.assert_called_once_with("weights_norm/fc2/weight", 12.0, 5)
mock_logger.writer.reset_mock()
wrapper = WeightsScalarHandler(model, tag="model", whitelist=["fc1"])
wrapper(mock_engine, mock_logger, Events.EPOCH_STARTED)
mock_logger.writer.add_scalar.assert_has_calls(
[
call("model/weights_norm/fc1/weight", 0.0, 5),
call("model/weights_norm/fc1/bias", 0.0, 5),
],
any_order=True,
)
assert mock_logger.writer.add_scalar.call_count == 2
mock_logger.writer.reset_mock()
def weight_selector(n, _):
return "bias" in n
wrapper = WeightsScalarHandler(model, tag="model", whitelist=weight_selector)
wrapper(mock_engine, mock_logger, Events.EPOCH_STARTED)
mock_logger.writer.add_scalar.assert_has_calls(
[
call("model/weights_norm/fc1/bias", 0.0, 5),
call("model/weights_norm/fc2/bias", pytest.approx(math.sqrt(12.0)), 5),
],
any_order=True,
)
assert mock_logger.writer.add_scalar.call_count == 2
def _test(tag=None):
wrapper = WeightsScalarHandler(model, tag=tag)
mock_logger = MagicMock(spec=TensorboardLogger)
mock_logger.writer = MagicMock()
mock_engine = MagicMock()
mock_engine.state = State()
mock_engine.state.epoch = 5
wrapper(mock_engine, mock_logger, Events.EPOCH_STARTED)
tag_prefix = f"{tag}/" if tag else ""
assert mock_logger.writer.add_scalar.call_count == 4
mock_logger.writer.add_scalar.assert_has_calls(
[
call(tag_prefix + "weights_norm/fc1/weight", 0.0, 5),
call(tag_prefix + "weights_norm/fc1/bias", 0.0, 5),
call(tag_prefix + "weights_norm/fc2/weight", 12.0, 5),
call(tag_prefix + "weights_norm/fc2/bias", math.sqrt(12.0), 5),
],
any_order=True,
)
def run(train_batch_size, val_batch_size, epochs, lr, momentum, log_dir):
train_loader, val_loader = get_data_loaders(train_batch_size,
val_batch_size)
model = Net()
device = "cpu"
if torch.cuda.is_available():
device = "cuda"
model.to(device) # Move model before creating optimizer
optimizer = SGD(model.parameters(), lr=lr, momentum=momentum)
criterion = nn.CrossEntropyLoss()
trainer = create_supervised_trainer(model,
optimizer,
criterion,
device=device)
trainer.logger = setup_logger("Trainer")
if sys.version_info > (3, ):
from ignite.contrib.metrics.gpu_info import GpuInfo
try:
GpuInfo().attach(trainer)
except RuntimeError:
print(
"INFO: By default, in this example it is possible to log GPU information (used memory, utilization). "
"As there is no pynvml python package installed, GPU information won't be logged. Otherwise, please "
"install it : `pip install pynvml`")
metrics = {"accuracy": Accuracy(), "loss": Loss(criterion)}
train_evaluator = create_supervised_evaluator(model,
metrics=metrics,
device=device)
train_evaluator.logger = setup_logger("Train Evaluator")
validation_evaluator = create_supervised_evaluator(model,
metrics=metrics,
device=device)
validation_evaluator.logger = setup_logger("Val Evaluator")
@trainer.on(Events.EPOCH_COMPLETED)
def compute_metrics(engine):
train_evaluator.run(train_loader)
validation_evaluator.run(val_loader)
tb_logger = TensorboardLogger(log_dir=log_dir)
tb_logger.attach_output_handler(
trainer,
event_name=Events.ITERATION_COMPLETED(every=100),
tag="training",
output_transform=lambda loss: {"batchloss": loss},
metric_names="all",
)
for tag, evaluator in [("training", train_evaluator),
("validation", validation_evaluator)]:
tb_logger.attach_output_handler(
evaluator,
event_name=Events.EPOCH_COMPLETED,
tag=tag,
metric_names=["loss", "accuracy"],
global_step_transform=global_step_from_engine(trainer),
)
tb_logger.attach_opt_params_handler(
trainer,
event_name=Events.ITERATION_COMPLETED(every=100),
optimizer=optimizer)
tb_logger.attach(trainer,
log_handler=WeightsScalarHandler(model),
event_name=Events.ITERATION_COMPLETED(every=100))
tb_logger.attach(trainer,
log_handler=WeightsHistHandler(model),
event_name=Events.EPOCH_COMPLETED(every=100))
tb_logger.attach(trainer,
log_handler=GradsScalarHandler(model),
event_name=Events.ITERATION_COMPLETED(every=100))
tb_logger.attach(trainer,
log_handler=GradsHistHandler(model),
event_name=Events.EPOCH_COMPLETED(every=100))
def score_function(engine):
return engine.state.metrics["accuracy"]
model_checkpoint = ModelCheckpoint(
log_dir,
n_saved=2,
filename_prefix="best",
score_function=score_function,
score_name="validation_accuracy",
global_step_transform=global_step_from_engine(trainer),
)
validation_evaluator.add_event_handler(Events.COMPLETED, model_checkpoint,
{"model": model})
# kick everything off
trainer.run(train_loader, max_epochs=epochs)
tb_logger.close()
def train_fold(fold, args):
# loggers
logging_logger = args.logging_logger
if args.tb_log:
tb_logger = args.tb_logger
num_classes = utils.problem_class[args.problem_type]
# init model
model = eval(args.model)(in_channels=3, num_classes=num_classes, bn=False)
model = nn.DataParallel(model, device_ids=args.device_ids).cuda()
# transform for train/valid data
train_transform, valid_transform = get_transform(args.model)
# loss function
loss_func = LossMulti(num_classes, args.jaccard_weight)
if args.semi:
loss_func_semi = LossMultiSemi(num_classes, args.jaccard_weight, args.semi_loss_alpha, args.semi_method)
# train/valid filenames
train_filenames, valid_filenames = utils.trainval_split(args.train_dir, fold)
# DataLoader and Dataset args
train_shuffle = True
train_ds_kwargs = {
'filenames': train_filenames,
'problem_type': args.problem_type,
'transform': train_transform,
'model': args.model,
'mode': 'train',
'semi': args.semi,
}
valid_num_workers = args.num_workers
valid_batch_size = args.batch_size
if 'TAPNet' in args.model:
# for TAPNet, cancel default shuffle, use self-defined shuffle in torch.Dataset instead
train_shuffle = False
train_ds_kwargs['batch_size'] = args.batch_size
train_ds_kwargs['mf'] = args.mf
if args.semi == True:
train_ds_kwargs['semi_method'] = args.semi_method
train_ds_kwargs['semi_percentage'] = args.semi_percentage
# additional valid dataset kws
valid_ds_kwargs = {
'filenames': valid_filenames,
'problem_type': args.problem_type,
'transform': valid_transform,
'model': args.model,
'mode': 'valid',
}
if 'TAPNet' in args.model:
# in validation, num_workers should be set to 0 for sequences
valid_num_workers = 0
# in validation, batch_size should be set to 1 for sequences
valid_batch_size = 1
valid_ds_kwargs['mf'] = args.mf
# train dataloader
train_loader = DataLoader(
dataset=RobotSegDataset(**train_ds_kwargs),
shuffle=train_shuffle, # set to False to disable pytorch dataset shuffle
num_workers=args.num_workers,
batch_size=args.batch_size,
pin_memory=True
)
# valid dataloader
valid_loader = DataLoader(
dataset=RobotSegDataset(**valid_ds_kwargs),
shuffle=False, # in validation, no need to shuffle
num_workers=valid_num_workers,
batch_size=valid_batch_size, # in valid time. have to use one image by one
pin_memory=True
)
# optimizer
optimizer = optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.weight_decay)
# optimizer = optim.SGD(model.parameters(), lr=args.lr, momentum=0.9,
# weight_decay=args.weight_decay, nesterov=True)
# ignite trainer process function
def train_step(engine, batch):
# set model to train
model.train()
# clear gradients
optimizer.zero_grad()
# additional params to feed into model
add_params = {}
inputs = batch['input'].cuda(non_blocking=True)
with torch.no_grad():
targets = batch['target'].cuda(non_blocking=True)
# for TAPNet, add attention maps
if 'TAPNet' in args.model:
add_params['attmap'] = batch['attmap'].cuda(non_blocking=True)
outputs = model(inputs, **add_params)
loss_kwargs = {}
if args.semi:
loss_kwargs['labeled'] = batch['labeled']
if args.semi_method == 'rev_flow':
loss_kwargs['optflow'] = batch['optflow']
loss = loss_func_semi(outputs, targets, **loss_kwargs)
else:
loss = loss_func(outputs, targets, **loss_kwargs)
loss.backward()
optimizer.step()
return_dict = {
'output': outputs,
'target': targets,
'loss_kwargs': loss_kwargs,
'loss': loss.item(),
}
# for TAPNet, update attention maps after each iteration
if 'TAPNet' in args.model:
# output_classes and target_classes: <b, h, w>
output_softmax_np = torch.softmax(outputs, dim=1).detach().cpu().numpy()
# update attention maps
train_loader.dataset.update_attmaps(output_softmax_np, batch['abs_idx'].numpy())
return_dict['attmap'] = add_params['attmap']
return return_dict
# init trainer
trainer = engine.Engine(train_step)
# lr scheduler and handler
# cyc_scheduler = optim.lr_scheduler.CyclicLR(optimizer, args.lr / 100, args.lr)
# lr_scheduler = c_handlers.param_scheduler.LRScheduler(cyc_scheduler)
# trainer.add_event_handler(engine.Events.ITERATION_COMPLETED, lr_scheduler)
step_scheduler = optim.lr_scheduler.StepLR(optimizer,
step_size=args.lr_decay_epochs, gamma=args.lr_decay)
lr_scheduler = c_handlers.param_scheduler.LRScheduler(step_scheduler)
trainer.add_event_handler(engine.Events.EPOCH_STARTED, lr_scheduler)
@trainer.on(engine.Events.STARTED)
def trainer_start_callback(engine):
logging_logger.info('training fold {}, {} train / {} valid files'. \
format(fold, len(train_filenames), len(valid_filenames)))
# resume training
if args.resume:
# ckpt for current fold fold_<fold>_model_<epoch>.pth
ckpt_dir = Path(args.ckpt_dir)
ckpt_filename = ckpt_dir.glob('fold_%d_model_[0-9]*.pth' % fold)[0]
res = re.match(r'fold_%d_model_(\d+).pth' % fold, ckpt_filename)
# restore epoch
engine.state.epoch = int(res.groups()[0])
# load model state dict
model.load_state_dict(torch.load(str(ckpt_filename)))
logging_logger.info('restore model [{}] from epoch {}.'.format(args.model, engine.state.epoch))
else:
logging_logger.info('train model [{}] from scratch'.format(args.model))
# record metrics history every epoch
engine.state.metrics_records = {}
@trainer.on(engine.Events.EPOCH_STARTED)
def trainer_epoch_start_callback(engine):
# log learning rate on pbar
train_pbar.log_message('model: %s, problem type: %s, fold: %d, lr: %.5f, batch size: %d' % \
(args.model, args.problem_type, fold, lr_scheduler.get_param(), args.batch_size))
# for TAPNet, change dataset schedule to random after the first epoch
if 'TAPNet' in args.model and engine.state.epoch > 1:
train_loader.dataset.set_dataset_schedule("shuffle")
@trainer.on(engine.Events.ITERATION_COMPLETED)
def trainer_iter_comp_callback(engine):
# logging_logger.info(engine.state.metrics)
pass
# monitor loss
# running average loss
train_ra_loss = imetrics.RunningAverage(output_transform=
lambda x: x['loss'], alpha=0.98)
train_ra_loss.attach(trainer, 'train_ra_loss')
# monitor train loss over epoch
if args.semi:
train_loss = imetrics.Loss(loss_func_semi, output_transform=lambda x: (x['output'], x['target'], x['loss_kwargs']))
else:
train_loss = imetrics.Loss(loss_func, output_transform=lambda x: (x['output'], x['target']))
train_loss.attach(trainer, 'train_loss')
# progress bar
train_pbar = c_handlers.ProgressBar(persist=True, dynamic_ncols=True)
train_metric_names = ['train_ra_loss']
train_pbar.attach(trainer, metric_names=train_metric_names)
# tensorboardX: log train info
if args.tb_log:
tb_logger.attach(trainer, log_handler=OptimizerParamsHandler(optimizer, 'lr'),
event_name=engine.Events.EPOCH_STARTED)
tb_logger.attach(trainer, log_handler=OutputHandler('train_iter', train_metric_names),
event_name=engine.Events.ITERATION_COMPLETED)
tb_logger.attach(trainer, log_handler=OutputHandler('train_epoch', ['train_loss']),
event_name=engine.Events.EPOCH_COMPLETED)
tb_logger.attach(trainer,
log_handler=WeightsScalarHandler(model, reduction=torch.norm),
event_name=engine.Events.ITERATION_COMPLETED)
# tb_logger.attach(trainer, log_handler=tb_log_train_vars,
# event_name=engine.Events.ITERATION_COMPLETED)
# ignite validator process function
def valid_step(engine, batch):
with torch.no_grad():
model.eval()
inputs = batch['input'].cuda(non_blocking=True)
targets = batch['target'].cuda(non_blocking=True)
# additional arguments
add_params = {}
# for TAPNet, add attention maps
if 'TAPNet' in args.model:
add_params['attmap'] = batch['attmap'].cuda(non_blocking=True)
# output logits
outputs = model(inputs, **add_params)
# loss
loss = loss_func(outputs, targets)
output_softmaxs = torch.softmax(outputs, dim=1)
output_argmaxs = output_softmaxs.argmax(dim=1)
# output_classes and target_classes: <b, h, w>
output_classes = output_argmaxs.cpu().numpy()
target_classes = targets.cpu().numpy()
# record current batch metrics
iou_mRecords = MetricRecord()
dice_mRecords = MetricRecord()
cm_b = np.zeros((num_classes, num_classes), dtype=np.uint32)
for output_class, target_class in zip(output_classes, target_classes):
# calculate metrics for each frame
# calculate using confusion matrix or dirctly using definition
cm = calculate_confusion_matrix_from_arrays(output_class, target_class, num_classes)
iou_mRecords.update_record(calculate_iou(cm))
dice_mRecords.update_record(calculate_dice(cm))
cm_b += cm
######## calculate directly using definition ##########
# iou_mRecords.update_record(iou_multi_np(target_class, output_class))
# dice_mRecords.update_record(dice_multi_np(target_class, output_class))
# accumulate batch metrics to engine state
engine.state.epoch_metrics['confusion_matrix'] += cm_b
engine.state.epoch_metrics['iou'].merge(iou_mRecords)
engine.state.epoch_metrics['dice'].merge(dice_mRecords)
return_dict = {
'loss': loss.item(),
'output': outputs,
'output_argmax': output_argmaxs,
'target': targets,
# for monitoring
'iou': iou_mRecords,
'dice': dice_mRecords,
}
if 'TAPNet' in args.model:
# for TAPNet, update attention maps after each iteration
valid_loader.dataset.update_attmaps(output_softmaxs.cpu().numpy(), batch['abs_idx'].numpy())
# for TAPNet, return extra internal values
return_dict['attmap'] = add_params['attmap']
# TODO: for TAPNet, return internal self-learned attention maps
return return_dict
# validator engine
validator = engine.Engine(valid_step)
# monitor loss
valid_ra_loss = imetrics.RunningAverage(output_transform=
lambda x: x['loss'], alpha=0.98)
valid_ra_loss.attach(validator, 'valid_ra_loss')
# monitor validation loss over epoch
valid_loss = imetrics.Loss(loss_func, output_transform=lambda x: (x['output'], x['target']))
valid_loss.attach(validator, 'valid_loss')
# monitor <data> mean metrics
valid_data_miou = imetrics.RunningAverage(output_transform=
lambda x: x['iou'].data_mean()['mean'], alpha=0.98)
valid_data_miou.attach(validator, 'mIoU')
valid_data_mdice = imetrics.RunningAverage(output_transform=
lambda x: x['dice'].data_mean()['mean'], alpha=0.98)
valid_data_mdice.attach(validator, 'mDice')
# show metrics on progress bar (after every iteration)
valid_pbar = c_handlers.ProgressBar(persist=True, dynamic_ncols=True)
valid_metric_names = ['valid_ra_loss', 'mIoU', 'mDice']
valid_pbar.attach(validator, metric_names=valid_metric_names)
# ## monitor ignite IoU (the same as iou we are using) ###
# cm = imetrics.ConfusionMatrix(num_classes,
# output_transform=lambda x: (x['output'], x['target']))
# imetrics.IoU(cm,
# ignore_index=0
# ).attach(validator, 'iou')
# # monitor ignite mean iou (over all classes even not exist in gt)
# mean_iou = imetrics.mIoU(cm,
# ignore_index=0
# ).attach(validator, 'mean_iou')
@validator.on(engine.Events.STARTED)
def validator_start_callback(engine):
pass
@validator.on(engine.Events.EPOCH_STARTED)
def validator_epoch_start_callback(engine):
engine.state.epoch_metrics = {
# directly use definition to calculate
'iou': MetricRecord(),
'dice': MetricRecord(),
'confusion_matrix': np.zeros((num_classes, num_classes), dtype=np.uint32),
}
# evaluate after iter finish
@validator.on(engine.Events.ITERATION_COMPLETED)
def validator_iter_comp_callback(engine):
pass
# evaluate after epoch finish
@validator.on(engine.Events.EPOCH_COMPLETED)
def validator_epoch_comp_callback(engine):
# log ignite metrics
# logging_logger.info(engine.state.metrics)
# ious = engine.state.metrics['iou']
# msg = 'IoU: '
# for ins_id, iou in enumerate(ious):
# msg += '{:d}: {:.3f}, '.format(ins_id + 1, iou)
# logging_logger.info(msg)
# logging_logger.info('nonzero mean IoU for all data: {:.3f}'.format(ious[ious > 0].mean()))
# log monitored epoch metrics
epoch_metrics = engine.state.epoch_metrics
######### NOTICE: Two metrics are available but different ##########
### 1. mean metrics for all data calculated by confusion matrix ####
'''
compared with using confusion_matrix[1:, 1:] in original code,
we use the full confusion matrix and only present non-background result
'''
confusion_matrix = epoch_metrics['confusion_matrix']# [1:, 1:]
ious = calculate_iou(confusion_matrix)
dices = calculate_dice(confusion_matrix)
mean_ious = np.mean(list(ious.values()))
mean_dices = np.mean(list(dices.values()))
std_ious = np.std(list(ious.values()))
std_dices = np.std(list(dices.values()))
logging_logger.info('mean IoU: %.3f, std: %.3f, for each class: %s' %
(mean_ious, std_ious, ious))
logging_logger.info('mean Dice: %.3f, std: %.3f, for each class: %s' %
(mean_dices, std_dices, dices))
### 2. mean metrics for all data calculated by definition ###
iou_data_mean = epoch_metrics['iou'].data_mean()
dice_data_mean = epoch_metrics['dice'].data_mean()
logging_logger.info('data (%d) mean IoU: %.3f, std: %.3f' %
(len(iou_data_mean['items']), iou_data_mean['mean'], iou_data_mean['std']))
logging_logger.info('data (%d) mean Dice: %.3f, std: %.3f' %
(len(dice_data_mean['items']), dice_data_mean['mean'], dice_data_mean['std']))
# record metrics in trainer every epoch
# trainer.state.metrics_records[trainer.state.epoch] = \
# {'miou': mean_ious, 'std_miou': std_ious,
# 'mdice': mean_dices, 'std_mdice': std_dices}
trainer.state.metrics_records[trainer.state.epoch] = \
{'miou': iou_data_mean['mean'], 'std_miou': iou_data_mean['std'],
'mdice': dice_data_mean['mean'], 'std_mdice': dice_data_mean['std']}
# log interal variables(attention maps, outputs, etc.) on validation
def tb_log_valid_iter_vars(engine, logger, event_name):
log_tag = 'valid_iter'
output = engine.state.output
batch_size = output['output'].shape[0]
res_grid = tvutils.make_grid(torch.cat([
output['output_argmax'].unsqueeze(1),
output['target'].unsqueeze(1),
]), padding=2,
normalize=False, # show origin image
nrow=batch_size).cpu()
logger.writer.add_image(tag='%s (outputs, targets)' % (log_tag), img_tensor=res_grid)
if 'TAPNet' in args.model:
# log attention maps and other internal values
inter_vals_grid = tvutils.make_grid(torch.cat([
output['attmap'],
]), padding=2, normalize=True, nrow=batch_size).cpu()
logger.writer.add_image(tag='%s internal vals' % (log_tag), img_tensor=inter_vals_grid)
def tb_log_valid_epoch_vars(engine, logger, event_name):
log_tag = 'valid_iter'
# log monitored epoch metrics
epoch_metrics = engine.state.epoch_metrics
confusion_matrix = epoch_metrics['confusion_matrix']# [1:, 1:]
ious = calculate_iou(confusion_matrix)
dices = calculate_dice(confusion_matrix)
mean_ious = np.mean(list(ious.values()))
mean_dices = np.mean(list(dices.values()))
logger.writer.add_scalar('mIoU', mean_ious, engine.state.epoch)
logger.writer.add_scalar('mIoU', mean_dices, engine.state.epoch)
if args.tb_log:
# log internal values
tb_logger.attach(validator, log_handler=tb_log_valid_iter_vars,
event_name=engine.Events.ITERATION_COMPLETED)
tb_logger.attach(validator, log_handler=tb_log_valid_epoch_vars,
event_name=engine.Events.EPOCH_COMPLETED)
# tb_logger.attach(validator, log_handler=OutputHandler('valid_iter', valid_metric_names),
# event_name=engine.Events.ITERATION_COMPLETED)
tb_logger.attach(validator, log_handler=OutputHandler('valid_epoch', ['valid_loss']),
event_name=engine.Events.EPOCH_COMPLETED)
# score function for model saving
ckpt_score_function = lambda engine: \
np.mean(list(calculate_iou(engine.state.epoch_metrics['confusion_matrix']).values()))
# ckpt_score_function = lambda engine: engine.state.epoch_metrics['iou'].data_mean()['mean']
ckpt_filename_prefix = 'fold_%d' % fold
# model saving handler
model_ckpt_handler = handlers.ModelCheckpoint(
dirname=args.model_save_dir,
filename_prefix=ckpt_filename_prefix,
score_function=ckpt_score_function,
create_dir=True,
require_empty=False,
save_as_state_dict=True,
atomic=True)
validator.add_event_handler(event_name=engine.Events.EPOCH_COMPLETED,
handler=model_ckpt_handler,
to_save={
'model': model,
})
# early stop
# trainer=trainer, but should be handled by validator
early_stopping = handlers.EarlyStopping(patience=args.es_patience,
score_function=ckpt_score_function,
trainer=trainer
)
validator.add_event_handler(event_name=engine.Events.EPOCH_COMPLETED,
handler=early_stopping)
# evaluate after epoch finish
@trainer.on(engine.Events.EPOCH_COMPLETED)
def trainer_epoch_comp_callback(engine):
validator.run(valid_loader)
trainer.run(train_loader, max_epochs=args.max_epochs)
if args.tb_log:
# close tb_logger
tb_logger.close()
return trainer.state.metrics_records
def setup(self, training_metrics):
def metric_name(n) -> str:
if n.endswith('Accuracy'):
n = 'acc'
else:
n = n[:-6] if n.endswith('Metric') else n
return n
def print_metrics(metrics) -> str:
rv = ''
metric_keys = sorted(k for k in metrics)
for k in metric_keys:
if k == 'Accuracy':
rv += f'{metric_name(k)}: {metrics[k]:.3}'
else:
rv += f'{metric_name(k)}: {metrics[k]:.6}'
return rv
if self.seed:
set_seed_everywhere(self.seed, self.cuda)
pbar = ProgressBar()
names = []
for k, v in training_metrics.items():
name = f'r{k}'
names.append(name)
RunningAverage(v).attach(self.trainer, name)
RunningAverage(None,
output_transform=lambda x: x[-1] * self.
loss_accumulation_steps).attach(self.trainer, 'rloss')
names.append('rloss')
pbar.attach(self.trainer, names)
pbar = ProgressBar()
pbar.attach(self.evaluator)
# A few events handler. To add / modify the events handler, you need to extend the __init__ method of RunnerABC
# Ignite provides the necessary abstractions and a furnished repository of useful tools
@self.trainer.on(Events.EPOCH_COMPLETED)
def log_validation_results(trainer):
self.evaluator.run(self.dataset_splits.val_data_loader())
metrics = self.evaluator.state.metrics
logger.info(
f"Validation Results - Epoch: {trainer.state.epoch} {print_metrics(metrics)}"
)
if self.scheduler:
self.scheduler.step(
metrics[self.loss_metric.__class__.__name__])
@self.trainer.on(Events.COMPLETED)
def log_test_results(trainer):
self.evaluator.run(self.dataset_splits.test_data_loader())
metrics = self.evaluator.state.metrics
logger.info(
f"Test Results - Epoch: {trainer.state.epoch} {print_metrics(metrics)}"
)
if self.tensorboard_logs:
tb_logger = TensorboardLogger(log_dir=self.tensorboard_logs)
tb_logger.attach(self.trainer,
log_handler=OutputHandler(
tag="training",
output_transform=lambda loss: {'loss': loss}),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(self.evaluator,
log_handler=OutputHandler(
tag="validation",
metric_names=["LossMetric"],
another_engine=self.trainer),
event_name=Events.EPOCH_COMPLETED)
tb_logger.attach(self.trainer,
log_handler=OptimizerParamsHandler(
self.optimizer),
event_name=Events.ITERATION_STARTED)
tb_logger.attach(self.trainer,
log_handler=WeightsScalarHandler(self.model),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(self.trainer,
log_handler=WeightsHistHandler(self.model),
event_name=Events.EPOCH_COMPLETED)
tb_logger.attach(self.trainer,
log_handler=GradsScalarHandler(self.model),
event_name=Events.ITERATION_COMPLETED)
# This is important to close the tensorboard file logger
@self.trainer.on(Events.COMPLETED)
def end_tensorboard(trainer):
logger.info("Training completed")
tb_logger.close()
if self.embeddings_name:
@self.trainer.on(Events.COMPLETED)
def log_embeddings(trainer):
if hasattr(self.model, self.embeddings_name) and hasattr(
self.dataset_splits, "vectorizer"):
logger.info(
f"Logging embeddings ({self.embeddings_name}) to Tensorboard!"
)
embeddings = getattr(self.model,
self.embeddings_name).weight.data
metadata = [
str(self.dataset_splits.vectorizer.data_vocab.
_id2token[token_index]).encode('utf-8')
for token_index in range(embeddings.shape[0])
]
self.writer.add_embedding(
mat=embeddings,
metadata=metadata,
global_step=self.trainer.state.epoch)
def train(epochs=500,
batch_size=32,
bptt_len=70,
lr=0.00025,
log_steps=200,
clip_grad=0.25,
log_dir="experiments"):
###################################################################
# Dataset
###################################################################
wt = wikitext103(batch_size=batch_size, bptt_len=bptt_len)
# wt = wikitext2(batch_size=batch_size, bptt_len=bptt_len)
###################################################################
# Configs
###################################################################
embedding_config = DropEmbedding.Hyperparams(len(wt.text_field.vocab) + 3,
ninp=512)
encoder_config = TransformerEncoder.Hyperparams(
att_num_units=[512, 512, 512, 512, 512, 512], max_ext=384)
###################################################################
# Models
###################################################################
base_embedding = DropEmbedding(embedding_config)
embedding = TransformerEmbedding(embedding=base_embedding,
max_length=bptt_len,
embedding_size=embedding_config.ninp,
use_positional_embedding=False)
encoder = TransformerEncoder(encoder_config)
model = TransformerLanguageModel(embedding, encoder)
model.init_weight()
###################################################################
# Loss
###################################################################
criterion = lm_criterion(in_features=encoder_config.att_num_units[-1],
vocab_size=len(wt.text_field.vocab))
###################################################################
# Parameters + Train ops
###################################################################
parameters = (list(model.parameters()) + list(criterion.parameters()))
tot_params = 0
for p in parameters:
tot_params += reduce(lambda x, y: x * y, p.size())
print("Total Parameters: ", tot_params)
opt = optim.Adam(parameters, lr=lr)
model.to(DEVICE)
criterion.to(DEVICE)
###################################################################
# Train + Evaluation
###################################################################
def train_step(engine, batch):
model.train()
opt.zero_grad()
text = batch.text.to(DEVICE).t().contiguous()
target = batch.target.to(DEVICE).t().contiguous()
out, out_past = model(text, engine.state.train_past)
engine.state.train_past = out_past
raw_loss = criterion(out.view(-1, out.size(2)), target.view(-1))
loss = raw_loss[1]
loss.backward()
nn.utils.clip_grad_norm_(parameters, clip_grad)
opt.step()
return {"train_loss": loss.item(), "train_ppl": loss.exp().item()}
def eval_step(engine, batch):
model.eval()
if not hasattr(engine.state, "eval_past"):
engine.state.eval_past = None
with torch.no_grad():
text = batch.text.to(DEVICE).t().contiguous()
target = batch.target.to(DEVICE).t().contiguous()
out, out_past = model(text, engine.state.eval_past)
engine.state.eval_past = out_past
raw_loss = criterion(out.view(-1, out.size(2)), target.view(-1))
loss = raw_loss[1]
return {"val_loss": loss.item()}
train_engine = Engine(train_step)
eval_engine = Engine(eval_step)
def reset_state(engine):
engine.state.train_past = None
def run_eval(_):
print("start running eval")
eval_engine.run(wt.valid_iter)
metrics = eval_engine.state.metrics
print("Validation loss: ", metrics["val_loss"], ", ppl: ",
np.exp(metrics["val_loss"]))
train_engine.add_event_handler(Events.EPOCH_STARTED, reset_state)
train_engine.add_event_handler(Events.EPOCH_COMPLETED, run_eval)
###################################################################
# LR Scheduler
###################################################################
cosine_scheduler = CosineAnnealingScheduler(opt.param_groups[0],
"lr",
0.0,
2.5e-4,
cycle_size=len(wt.train_iter))
warmup_scheduler = create_lr_scheduler_with_warmup(cosine_scheduler, 0.0,
2.5e-4, 200)
train_engine.add_event_handler(Events.ITERATION_STARTED, warmup_scheduler)
###################################################################
# Metrics
###################################################################
RunningAverage(output_transform=lambda x: x["train_ppl"]).attach(
train_engine, "train_ppl")
RunningAverage(output_transform=lambda x: x["train_loss"]).attach(
train_engine, "train_loss")
RunningAverage(output_transform=lambda x: x["val_loss"]).attach(
eval_engine, "val_loss")
progress_bar = ProgressBar(persist=True)
progress_bar.attach(train_engine, ["train_ppl", "train_loss"])
progress_bar_val = ProgressBar(persist=True)
progress_bar_val.attach(eval_engine, ["val_loss"])
###################################################################
# Tensorboard
###################################################################
tb_logger = TensorboardLogger(log_dir=log_dir)
def stepn_logger(num_steps, handler):
def logger_runner(engine, log_handler, event_name):
if engine.state.iteration % num_steps == 0:
handler(engine, log_handler, event_name)
return logger_runner
tb_logger.attach(train_engine,
log_handler=stepn_logger(
log_steps,
OutputHandler(tag="training",
output_transform=lambda loss: loss)),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(eval_engine,
log_handler=OutputHandler(
tag="validation",
output_transform=lambda loss: loss,
another_engine=train_engine),
event_name=Events.EPOCH_COMPLETED)
tb_logger.attach(train_engine,
log_handler=stepn_logger(log_steps,
OptimizerParamsHandler(opt)),
event_name=Events.ITERATION_STARTED)
tb_logger.attach(train_engine,
log_handler=stepn_logger(log_steps,
WeightsScalarHandler(model)),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(train_engine,
log_handler=stepn_logger(log_steps,
GradsScalarHandler(model)),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(train_engine,
log_handler=stepn_logger(500, WeightsHistHandler(model)),
event_name=Events.ITERATION_COMPLETED)
tb_logger.attach(train_engine,
log_handler=stepn_logger(500, GradsHistHandler(model)),
event_name=Events.ITERATION_COMPLETED)
try:
train_engine.run(wt.train_iter, max_epochs=epochs)
except Exception:
pass
finally:
tb_logger.close()