def get_epochs_to_test(self):
if self.args.test_all_epochs:
# Get all saved points and test them
epochs_tested = [
list(
range(self.args.nb_epochs_per_saving, self.args.nb_epochs,
self.args.nb_epochs_per_saving)) +
[self.args.nb_epochs - 1] for _ in range(self.args.nb_folds)
]
elif self.args.test_best_epoch:
# Get the best point of each fold according to a certain metric (early stopping)
metric = self.args.test_best_epoch
h_val = History.load_from_dir(
self.args.checkpoint_dir,
"Validation_%s" % (self.args.exp_name or ""),
self.args.nb_folds - 1, self.args.nb_epochs - 1)
epochs_tested = h_val.get_best_epochs(metric,
highest=True).reshape(-1, 1)
else:
# Get the last point and test it, for each fold
epochs_tested = [[self.args.nb_epochs - 1]
for _ in range(self.args.nb_folds)]
return epochs_tested
def training(self, manager: AbstractDataManager, nb_epochs: int, checkpointdir=None,
fold_index=None, epoch_index=None,
scheduler=None, with_validation=True, with_visualization=False,
nb_epochs_per_saving=1, exp_name=None, standard_optim=True,
gpu_time_profiling=False, **kwargs_train):
""" Train the model.
Parameters
----------
manager: a pynet DataManager
a manager containing the train and validation data.
nb_epochs: int, default 100
the number of epochs.
checkpointdir: str, default None
a destination folder where intermediate models/historues will be
saved.
fold_index: int or [int] default None
the index(es) of the fold(s) to use for the training, default use all the
available folds.
epoch_index: int, default None
the iteration where to start the counting from
scheduler: torch.optim.lr_scheduler, default None
a scheduler used to reduce the learning rate.
with_validation: bool, default True
if set use the validation dataset.
with_visualization: bool, default False,
whether it uses a visualizer that will plot the losses/metrics/images in a WebApp framework
during the training process
nb_epochs_per_saving: int, default 1,
the number of epochs after which the model+optimizer's parameters are saved
exp_name: str, default None
the experience name that will be launched
Returns
-------
train_history, valid_history: History
the train/validation history.
"""
train_history = History(name="Train_%s"%(exp_name or ""))
if with_validation is not None:
valid_history = History(name="Validation_%s"%(exp_name or ""))
else:
valid_history = None
train_visualizer, valid_visualizer = None, None
if with_visualization:
train_visualizer = Visualizer(train_history)
if with_validation:
valid_visualizer = Visualizer(valid_history, offset_win=10)
print(self.loss)
print(self.optimizer)
folds = range(manager.get_nb_folds())
if fold_index is not None:
if isinstance(fold_index, int):
folds = [fold_index]
elif isinstance(fold_index, list):
folds = fold_index
if epoch_index is None:
epoch_index = 0
init_optim_state = deepcopy(self.optimizer.state_dict())
init_model_state = deepcopy(self.model.state_dict())
if scheduler is not None:
init_scheduler_state = deepcopy(scheduler.state_dict())
for fold in folds:
# Initialize everything before optimizing on a new fold
self.optimizer.load_state_dict(init_optim_state)
self.model.load_state_dict(init_model_state)
if scheduler is not None:
scheduler.load_state_dict(init_scheduler_state)
loader = manager.get_dataloader(
train=True,
validation=True,
fold_index=fold)
for epoch in range(nb_epochs):
self.notify_observers("before_epoch", epoch=epoch, fold=fold)
loss, values = self.train(loader.train, train_visualizer, fold, epoch,
standard_optim=standard_optim,
gpu_time_profiling=gpu_time_profiling, **kwargs_train)
train_history.log((fold, epoch+epoch_index), loss=loss, **values)
train_history.summary()
if scheduler is not None:
scheduler.step()
print('Scheduler lr: {}'.format(scheduler.get_lr()), flush=True)
print('Optimizer lr: %f'%self.optimizer.param_groups[0]['lr'], flush=True)
if checkpointdir is not None and (epoch % nb_epochs_per_saving == 0 or epoch == nb_epochs-1) \
and epoch > 0:
checkpoint(
model=self.model,
epoch=epoch+epoch_index,
fold=fold,
outdir=checkpointdir,
name=exp_name,
optimizer=self.optimizer)
train_history.save(
outdir=checkpointdir,
epoch=epoch+epoch_index,
fold=fold)
if with_validation:
_, _, _, loss, values = self.test(loader.validation,
standard_optim=standard_optim, **kwargs_train)
valid_history.log((fold, epoch+epoch_index), validation_loss=loss, **values)
valid_history.summary()
if valid_visualizer is not None:
valid_visualizer.refresh_current_metrics()
if checkpointdir is not None and (epoch % nb_epochs_per_saving == 0 or epoch == nb_epochs-1) \
and epoch > 0:
valid_history.save(
outdir=checkpointdir,
epoch=epoch+epoch_index,
fold=fold)
self.notify_observers("after_epoch", epoch=epoch, fold=fold)
return train_history, valid_history
def training(self,
manager,
nb_epochs,
checkpointdir=None,
fold_index=None,
scheduler=None,
with_validation=True,
save_after_epochs=1,
add_labels=False):
""" Train the model.
Parameters
----------
manager: a pynet DataManager
a manager containing the train and validation data.
nb_epochs: int, default 100
the number of epochs.
checkpointdir: str, default None
a destination folder where intermediate models/historues will be
saved.
fold_index: int, default None
the index of the fold to use for the training, default use all the
available folds.
scheduler: torch.optim.lr_scheduler, default None
a scheduler used to reduce the learning rate.
with_validation: bool, default True
if set use the validation dataset.
save_after_epochs: int, default 1
determines when the model is saved and represents the number of
epochs before saving.
Returns
-------
train_history, valid_history: History
the train/validation history.
"""
if self.resume and "scheduler" in self.checkpoint:
scheduler.load_state_dict(self.checkpoint["scheduler"])
if checkpointdir is not None and not os.path.isdir(checkpointdir):
os.mkdir(checkpointdir)
train_history = History(name="train")
if with_validation is not None:
valid_history = History(name="validation")
else:
valid_history = None
logger.info("Loss function {0}.".format(self.loss))
logger.info("Optimizer function {0}.".format(self.optimizer))
folds = range(manager.number_of_folds)
if fold_index is not None:
folds = [fold_index]
for fold in folds:
logger.debug("Running fold {0}...".format(fold))
reset_weights(self.model, self.checkpoint)
loaders = manager.get_dataloader(train=True,
validation=with_validation,
fold_index=fold)
for epoch in range(nb_epochs):
logger.debug("Running epoch {0}:".format(fold))
logger.debug(" notify observers with signal 'before_epoch'.")
self.notify_observers("before_epoch", epoch=epoch, fold=fold)
observers_kwargs = {}
logger.debug(" train.")
loss, values = self.train(loaders.train)
observers_kwargs["loss"] = loss
observers_kwargs.update(values)
if scheduler is not None:
logger.debug(" update scheduler.")
scheduler.step(loss)
logger.debug(" update train history.")
train_history.log((fold, epoch), loss=loss, **values)
train_history.summary()
if (checkpointdir is not None
and epoch % save_after_epochs == 0):
logger.debug(" create checkpoint.")
checkpoint(model=self.model,
epoch=epoch,
fold=fold,
outdir=checkpointdir,
optimizer=self.optimizer,
scheduler=scheduler)
train_history.save(outdir=checkpointdir,
epoch=epoch,
fold=fold)
if with_validation:
logger.debug(" validation.")
y_pred, loss, values = self.test(loaders.validation)
observers_kwargs["val_loss"] = loss
observers_kwargs.update(
dict(("val_{0}".format(key), val)
for key, val in values.items()))
observers_kwargs["val_pred"] = y_pred
logger.debug(" update validation history.")
valid_history.log((fold, epoch), loss=loss, **values)
valid_history.summary()
if (checkpointdir is not None
and epoch % save_after_epochs == 0):
logger.debug(" create checkpoint.")
valid_history.save(outdir=checkpointdir,
epoch=epoch,
fold=fold)
logger.debug(" notify observers with signal 'after_epoch'.")
self.notify_observers("after_epoch",
epoch=epoch,
fold=fold,
**observers_kwargs)
logger.debug("End epoch.".format(fold))
logger.debug("End fold.")
return train_history, valid_history
"num_classes": 4,
"activation": "relu",
"normalization": "group_normalization",
"mode": "trilinear",
"with_vae": True,
"debug": False
}
if os.path.isfile(trained_model):
nvnet = NvNetSegmenter(nvnet_kwargs,
optimizer_name="Adam",
learning_rate=1e-4,
weight_decay=1e-5,
loss=my_loss,
pretrained=trained_model,
use_cuda=True)
train_history = History.load(os.path.join(outdir, "train_0_epoch_9.pkl"))
valid_history = History.load(
os.path.join(outdir, "validation_0_epoch_9.pkl"))
else:
nvnet = NvNetSegmenter(nvnet_kwargs,
optimizer_name="Adam",
learning_rate=1e-4,
weight_decay=1e-5,
loss=my_loss,
use_cuda=True)
scheduler = lr_scheduler.ReduceLROnPlateau(optimizer=nvnet.optimizer,
mode="min",
factor=0.5,
patience=5)
train_history, valid_history = nvnet.training(
manager=manager,
model=net,
metrics=["accuracy"])
test_history, train_history = cl.training(manager=manager,
nb_epochs=3,
checkpointdir="/tmp/pynet",
fold_index=0,
with_validation=True)
#############################################################################
# You can reload the optimization history at any time and any step.
from pprint import pprint
from pynet.history import History
from pynet.plotting import plot_history
history = History.load("/tmp/pynet/train_0_epoch_2.pkl")
print(history)
plot_history(history)
#############################################################################
# And now predict the labels on the test set.
import numpy as np
from sklearn.metrics import classification_report
from pynet.plotting import plot_data
y_pred, X, y_true, loss, values = cl.testing(manager=manager,
with_logit=True,
predict=True)
pprint(data.labels)
print(classification_report(y_true, y_pred, target_names=data.labels.values()))
pb=pb,
hyper=hyper,
n_finetuning=n_finetuning,
block=b,
f=fold,
e=e))) for fold in range(folds)
]
else:
if CV:
if pb == 'Alzheimer':
filename = "Validation_DenseNet_{pb}_{db}_CV_%i_epoch_{e}.pkl"
else:
filename = "Validation_DenseNet_{pb}_{db}_%i_epoch_{e}.pkl"
results[db][name][n_finetuning] = History.load(
os.path.join(root, path.format(n=N_pretraining,
n_finetune=n_finetuning, pb=pb), filename.
format(db=db, pb=pb, e=e)), folds=list(range(folds))). \
to_dict(patterns_to_del=patterns_to_del)
else:
filename = "Test_DenseNet_{pb}_{db}_fold{f}_epoch{e}.pkl"
results[db][name][n_finetuning] = [
get_pickle_obj(
os.path.join(
root,
path.format(n=N_pretraining,
n_finetune=n_finetuning,
pb=pb),
filename.format(db=db, pb=pb, f=fold, e=e)))
for fold in range(folds)
]
def training(self,
manager,
nb_epochs,
checkpointdir=None,
fold_index=None,
scheduler=None,
with_validation=True):
""" Train the model.
Parameters
----------
manager: a pynet DataManager
a manager containing the train and validation data.
nb_epochs: int, default 100
the number of epochs.
checkpointdir: str, default None
a destination folder where intermediate models/historues will be
saved.
fold_index: int, default None
the index of the fold to use for the training, default use all the
available folds.
scheduler: torch.optim.lr_scheduler, default None
a scheduler used to reduce the learning rate.
with_validation: bool, default True
if set use the validation dataset.
Returns
-------
train_history, valid_history: History
the train/validation history.
"""
if checkpointdir is not None and not os.path.isdir(checkpointdir):
os.mkdir(checkpointdir)
train_history = History(name="train")
if with_validation is not None:
valid_history = History(name="validation")
else:
valid_history = None
print(self.loss)
print(self.optimizer)
folds = range(manager.number_of_folds)
if fold_index is not None:
folds = [fold_index]
for fold in folds:
reset_weights(self.model)
loaders = manager.get_dataloader(train=True,
validation=True,
fold_index=fold)
for epoch in range(nb_epochs):
self.notify_observers("before_epoch", epoch=epoch, fold=fold)
observers_kwargs = {}
loss, values = self.train(loaders.train)
observers_kwargs["loss"] = loss
observers_kwargs.update(values)
if scheduler is not None:
scheduler.step(loss)
train_history.log((fold, epoch), loss=loss, **values)
train_history.summary()
if checkpointdir is not None:
checkpoint(model=self.model,
epoch=epoch,
fold=fold,
outdir=checkpointdir,
optimizer=self.optimizer)
train_history.save(outdir=checkpointdir,
epoch=epoch,
fold=fold)
if with_validation:
_, loss, values = self.test(loaders.validation)
observers_kwargs["val_loss"] = loss
observers_kwargs.update(
dict(("val_{0}".format(key), val)
for key, val in values.items()))
valid_history.log((fold, epoch), loss=loss, **values)
valid_history.summary()
if checkpointdir is not None:
valid_history.save(outdir=checkpointdir,
epoch=epoch,
fold=fold)
self.notify_observers("after_epoch",
epoch=epoch,
fold=fold,
**observers_kwargs)
return train_history, valid_history
test_history, train_history, valid_history = training(net=net,
dataset=dataset,
optimizer=optim.Adam(
net.parameters(),
lr=0.01),
criterion=my_loss,
nb_epochs=3,
metrics={"mse": my_loss},
use_cuda=False,
outdir="/tmp/pynet",
verbose=1)
#############################################################################
# You can reload the optimization history at any time and any step
from pprint import pprint
from pynet.history import History
valid_history = History.load("/tmp/pynet/history/valid_1_epoch_3.pkl")
pprint(valid_history.history)
pprint(valid_history["loss"])
#############################################################################
# You can finally display the optimization cost
from pynet.plotting import plot_data
x, y = valid_history["loss"]
plot_data(y)
