def test_loss_dict(self):
log_stream = StringIO()
logging.basicConfig(stream=log_stream, level=logging.INFO)
key_to_handler = 'test_logging'
key_to_print = 'myLoss1'
# set up engine
def _train_func(engine, batch):
return torch.tensor(0.0)
engine = Engine(_train_func)
# set up testing handler
stats_handler = StatsHandler(
name=key_to_handler, output_transform=lambda x: {key_to_print: x})
stats_handler.attach(engine)
engine.run(range(3), max_epochs=2)
# check logging output
output_str = log_stream.getvalue()
grep = re.compile('.*{}.*'.format(key_to_handler))
has_key_word = re.compile('.*{}.*'.format(key_to_print))
for idx, line in enumerate(output_str.split('\n')):
if grep.match(line):
if idx in [1, 2, 3, 6, 7, 8]:
self.assertTrue(has_key_word.match(line))
def test_metrics_print(self):
log_stream = StringIO()
logging.basicConfig(stream=log_stream, level=logging.INFO)
key_to_handler = 'test_logging'
key_to_print = 'testing_metric'
# set up engine
def _train_func(engine, batch):
return torch.tensor(0.0)
engine = Engine(_train_func)
# set up dummy metric
@engine.on(Events.EPOCH_COMPLETED)
def _update_metric(engine):
current_metric = engine.state.metrics.get(key_to_print, 0.1)
engine.state.metrics[key_to_print] = current_metric + 0.1
# set up testing handler
stats_handler = StatsHandler(name=key_to_handler)
stats_handler.attach(engine)
engine.run(range(3), max_epochs=2)
# check logging output
output_str = log_stream.getvalue()
grep = re.compile('.*{}.*'.format(key_to_handler))
has_key_word = re.compile('.*{}.*'.format(key_to_print))
for idx, line in enumerate(output_str.split('\n')):
if grep.match(line):
if idx in [5, 10]:
self.assertTrue(has_key_word.match(line))
n_saved=10,
require_empty=False)
trainer.add_event_handler(event_name=Events.EPOCH_COMPLETED,
handler=checkpoint_handler,
to_save={
'net': net,
'opt': opt
})
dice_metric = MeanDice(add_sigmoid=True,
output_transform=lambda output:
(output[0][0], output[2]))
dice_metric.attach(trainer, "Training Dice")
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
stats_logger = StatsHandler()
stats_logger.attach(trainer)
@trainer.on(Events.EPOCH_COMPLETED)
def log_training_loss(engine):
# log loss to tensorboard with second item of engine.state.output, loss.item() from output_transform
writer.add_scalar('Loss/train', engine.state.output[1], engine.state.epoch)
# tensor of ones to use where for converting labels to zero and ones
ones = torch.ones(engine.state.batch[1][0].shape, dtype=torch.int32)
first_output_tensor = engine.state.output[0][1][0].detach().cpu()
# log model output to tensorboard, as three dimensional tensor with no channels dimension
img2tensorboard.add_animated_gif_no_channels(writer,
"first_output_final_batch",
first_output_tensor, 64, 255,
with torch.no_grad():
seg_probs = sliding_window_inference(img, roi_size, sw_batch_size, net,
device)
return seg_probs, seg.to(device)
evaluator = Engine(_sliding_window_processor)
# add evaluation metric to the evaluator engine
MeanDice(add_sigmoid=True, to_onehot_y=False).attach(evaluator, 'Mean_Dice')
# StatsHandler prints loss at every iteration and print metrics at every epoch,
# we don't need to print loss for evaluator, so just print metrics, user can also customize print functions
val_stats_handler = StatsHandler(
name='evaluator',
output_transform=lambda x:
None # no need to print loss value, so disable per iteration output
)
val_stats_handler.attach(evaluator)
# for the arrary data format, assume the 3rd item of batch data is the meta_data
file_saver = SegmentationSaver(
output_path='tempdir',
output_ext='.nii.gz',
output_postfix='seg',
name='evaluator',
batch_transform=lambda x: x[2],
output_transform=lambda output: predict_segmentation(output[0]))
file_saver.attach(evaluator)
# the model was trained by "unet_training_array" exmple
# adding checkpoint handler to save models (network params and optimizer stats) during training
checkpoint_handler = ModelCheckpoint('./runs/',
'net',
n_saved=10,
require_empty=False)
trainer.add_event_handler(event_name=Events.EPOCH_COMPLETED,
handler=checkpoint_handler,
to_save={
'net': net,
'opt': opt
})
# StatsHandler prints loss at every iteration and print metrics at every epoch,
# we don't set metrics for trainer here, so just print loss, user can also customize print functions
# and can use output_transform to convert engine.state.output if it's not loss value
train_stats_handler = StatsHandler(name='trainer')
train_stats_handler.attach(trainer)
# TensorBoardStatsHandler plots loss at every iteration and plots metrics at every epoch, same as StatsHandler
train_tensorboard_stats_handler = TensorBoardStatsHandler()
train_tensorboard_stats_handler.attach(trainer)
# Set parameters for validation
validation_every_n_epochs = 1
metric_name = 'Accuracy'
# add evaluation metric to the evaluator engine
val_metrics = {metric_name: Accuracy()}
# ignite evaluator expects batch=(img, label) and returns output=(y_pred, y) at every iteration,
# user can add output_transform to return other values
evaluator = create_supervised_evaluator(net,