def set_up_training(project_directory, config, data_config,
load_pretrained_model):
# Get model
if load_pretrained_model:
model = Trainer().load(from_directory=project_directory,
filename='Weights/checkpoint.pytorch').model
else:
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
criterion = SorensenDiceLoss()
loss_train = LossWrapper(criterion=criterion,
transforms=Compose(ApplyAndRemoveMask(),
InvertTarget()))
loss_val = LossWrapper(criterion=criterion,
transforms=Compose(RemoveSegmentationFromTarget(),
ApplyAndRemoveMask(),
InvertTarget()))
# Build trainer and validation metric
logger.info("Building trainer.")
smoothness = 0.95
offsets = data_config['volume_config']['segmentation']['affinity_config'][
'offsets']
metric = ArandErrorFromMulticut(average_slices=False,
use_2d_ws=True,
n_threads=8,
weight_edges=True,
offsets=offsets)
trainer = Trainer(model)\
.save_every((1000, 'iterations'),
to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss_train)\
.build_validation_criterion(loss_val)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=1)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.98,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))\
.register_callback(GarbageCollection())
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations'),
log_histograms_every='never').observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def set_up_training(project_directory, config, data_config, criterion, balance,
load_pretrained_model):
# Get model
if load_pretrained_model:
model = Trainer().load(from_directory=project_directory,
filename='Weights/checkpoint.pytorch').model
else:
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
# TODO
logger.info("Using criterion: %s" % criterion)
# TODO this should go somewhere more prominent
affinity_offsets = data_config['volume_config']['segmentation'][
'affinity_offsets']
# TODO implement affinities on gpu again ?!
criterion = CRITERIA[criterion]
loss = LossWrapper(
criterion=criterion(),
transforms=Compose(MaskTransitionToIgnoreLabel(affinity_offsets),
RemoveSegmentationFromTarget(), InvertTarget()),
weight_function=BalanceAffinities(
ignore_label=0, offsets=affinity_offsets) if balance else None)
# Build trainer and validation metric
logger.info("Building trainer.")
smoothness = 0.95
# use multicut pipeline for validation
metric = ArandErrorFromSegmentationPipeline(
local_affinity_multicut_from_wsdt2d(n_threads=10, time_limit=120))
trainer = Trainer(model)\
.save_every((1000, 'iterations'), to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=1)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.98,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations')).observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def load_model(args):
trainer = Trainer()
trainer.load(from_directory=args.load_directory, best=False)
# trainer.load(from_directory=args.load_directory, best=False)
trainer.set_max_num_epochs(args.epochs + trainer.epoch_count)
model = trainer.model
trainer.build_logger(TensorboardLogger(log_scalars_every=(1, 'iteration'),
log_images_every='never'),
log_directory=args.save_directory)
trainer.save_to_directory(args.save_directory)
return (model, trainer)
def set_up_training(project_directory, config, data_config,
load_pretrained_model):
# Get model
if load_pretrained_model:
model = Trainer().load(from_directory=project_directory,
filename='Weights/checkpoint.pytorch').model
else:
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
affinity_offsets = data_config['volume_config']['segmentation'][
'affinity_offsets']
loss = LossWrapper(criterion=SorensenDiceLoss(),
transforms=Compose(
MaskTransitionToIgnoreLabel(affinity_offsets),
RemoveSegmentationFromTarget(), InvertTarget()))
# Build trainer and validation metric
logger.info("Building trainer.")
smoothness = 0.95
# use multicut pipeline for validation
# metric = ArandErrorFromSegmentationPipeline(local_affinity_multicut_from_wsdt2d(n_threads=10,
# time_limit=120))
# use damws for validation
stride = [2, 10, 10]
metric = ArandErrorFromSegmentationPipeline(
DamWatershed(affinity_offsets, stride, randomize_bounds=False))
trainer = Trainer(model)\
.save_every((1000, 'iterations'), to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=1)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.98,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations')).observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def set_up_training(project_directory, config, data_config):
# Get model
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
criterion = SorensenDiceLoss()
loss_train = LossWrapper(criterion=criterion, transforms=InvertTarget())
loss_val = LossWrapper(criterion=criterion,
transforms=Compose(RemoveSegmentationFromTarget(),
InvertTarget()))
# Build trainer and validation metric
logger.info("Building trainer.")
smoothness = 0.75
offsets = data_config['volume_config']['segmentation']['affinity_config'][
'offsets']
strides = [1, 10, 10]
metric = ArandErrorFromMWS(average_slices=False,
offsets=offsets,
strides=strides,
randomize_strides=False)
trainer = Trainer(model)\
.save_every((1000, 'iterations'),
to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss_train)\
.build_validation_criterion(loss_val)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=1)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness,
verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.99,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))\
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations'),
log_histograms_every='never').observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def set_up_training(project_directory, config, data_config,
load_pretrained_model, max_iters):
# Get model
if load_pretrained_model:
model = Trainer().load(from_directory=project_directory,
filename='Weights/checkpoint.pytorch').model
else:
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
loss = LossWrapper(criterion=SorensenDiceLoss(),
transforms=Compose(MaskIgnoreLabel(),
RemoveSegmentationFromTarget()))
# TODO loss transforms:
# - Invert Target ???
# Build trainer and validation metric
logger.info("Building trainer.")
# smoothness = 0.95
# TODO set up validation ?!
trainer = Trainer(model)\
.save_every((1000, 'iterations'), to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.register_callback(ManualLR(decay_specs=[((k * 100, 'iterations'), 0.99)
for k in range(1, max_iters // 100)]))
# .validate_every((100, 'iterations'), for_num_iterations=1)\
# .register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
# .build_metric(metric)\
# .register_callback(AutoLR(factor=0.98,
# patience='100 iterations',
# monitor_while='validating',
# monitor_momentum=smoothness,
# consider_improvement_with_respect_to='previous'))
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations')) # .observe_states(
# ['validation_input', 'validation_prediction, validation_target'],
# observe_while='validating'
# )
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def my_train(load, folder):
click.echo('starting training')
os.makedirs(folder, exist_ok=True)
# joint_transform = Compose(
# RandomRotate(),
# RandomTranspose(),
# RandomFlip()
# )
# setup logger
os.makedirs('derived_data/log', exist_ok=True)
Logger.instance().setup('derived_data/log')
vae = Vae()
ds = HemoDataset(root_folder=root_folder, image_transform=None, training=True)
train_loader = torch.utils.data.DataLoader(ds, batch_size=1536, num_workers=8)
# Build trainer
trainer = Trainer(vae)
trainer.save_to_directory(folder)
if load:
trainer.load()
# trainer.cuda(devices=[0, 1])
trainer.cuda()
trainer.build_criterion(vae.loss_function())
trainer.build_optimizer('Adam', lr=0.001)
# trainer.validate_every((2, 'epochs'))
trainer.save_every((1, 'epochs'))
trainer.set_max_num_epochs(100)
trainer.build_logger(TensorboardLogger(log_scalars_every=(1, 'iteration'),
log_images_every='never',
# log_images_every=(1, 'iteration'),
log_directory=folder))
# Bind loaders
trainer.bind_loader('train', train_loader, num_inputs=1, num_targets=1)
# bind callbacks
trainer.register_callback(GarbageCollection(), trigger='end_of_training_iteration')
trainer.register_callback(ShowMinimalConsoleInfo(), trigger='end_of_training_iteration')
# trainer.bind_loader('train', train_loader, num_inputs=3, num_targets=1)
trainer.fit()
pushover_notification.send('embeddings generated')
def set_up_training(project_directory, config, data_config,
load_pretrained_model):
# Get model
if load_pretrained_model:
model = Trainer().load(from_directory=project_directory,
filename='Weights/checkpoint.pytorch').model
else:
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
loss = dice_loss()
loss_val = dice_loss(is_val=True)
metric = mws_metric()
# metric = loss_val
# Build trainer and validation metric
logger.info("Building trainer.")
smoothness = 0.9
trainer = Trainer(model)\
.save_every((1000, 'iterations'),
to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss)\
.build_validation_criterion(loss_val)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=5)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.98,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))\
.register_callback(GarbageCollection())\
logger.info("Building logger.")
# Build logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations'),
log_histograms_every='never').observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
def run(args):
dataset = RorschachWrapper()
save_args(args) # save command line to a file for reference
train_loader = rorschach_cgan_data_loader(args,
dataset=dataset) # get the data
# todo
model = patchCWGANModel(args,
discriminator=patchCDiscriminatorNetwork(args),
generator=CGeneratorNetwork(args))
# Build trainer
trainer = Trainer(model)
trainer.build_criterion(
CWGANDiscriminatorLoss(penalty_weight=args.penalty_weight,
model=model))
trainer.build_optimizer('Adam',
model.discriminator.parameters(),
lr=args.discriminator_lr)
trainer.save_every((1, 'epochs'))
trainer.save_to_directory(args.save_directory)
trainer.set_max_num_epochs(args.epochs)
trainer.register_callback(CGenerateDataCallback(args, dataset=dataset))
trainer.register_callback(
CGeneratorTrainingCallback(args,
parameters=model.generator.parameters(),
criterion=WGANGeneratorLoss(),
dataset=dataset))
trainer.bind_loader('train', train_loader, num_inputs=2)
# Custom logging configuration so it knows to log our images
logger = TensorboardLogger(log_scalars_every=(1, 'iteration'),
log_images_every=(args.log_image_frequency,
'iteration'))
trainer.build_logger(logger, log_directory=args.save_directory)
logger.observe_state('generated_images')
logger.observe_state('real_images')
logger._trainer_states_being_observed_while_training.remove(
'training_inputs')
if args.cuda:
trainer.cuda()
# Go!
trainer.fit()
def run(args):
save_args(args) # save command line to a file for reference
train_loader = mnist_data_loader(args) # get the data
model = GANModel(args,
discriminator=DiscriminatorNetwork(args),
generator=GeneratorNetwork(args))
# Build trainer
trainer = Trainer(model)
trainer.build_criterion(
WGANDiscriminatorLoss(penalty_weight=args.penalty_weight, model=model))
trainer.build_optimizer('Adam',
model.discriminator.parameters(),
lr=args.discriminator_lr)
trainer.save_every((1, 'epochs'))
trainer.save_to_directory(args.save_directory)
trainer.set_max_num_epochs(args.epochs)
trainer.register_callback(GenerateDataCallback(args))
trainer.register_callback(
GeneratorTrainingCallback(args,
parameters=model.generator.parameters(),
criterion=WGANGeneratorLoss()))
trainer.bind_loader('train', train_loader)
# Custom logging configuration so it knows to log our images
logger = TensorboardLogger(log_scalars_every=(1, 'iteration'),
log_images_every=(args.log_image_frequency,
'iteration'))
trainer.build_logger(logger, log_directory=args.save_directory)
logger.observe_state('generated_images')
logger.observe_state('real_images')
logger._trainer_states_being_observed_while_training.remove(
'training_inputs')
if args.cuda:
trainer.cuda()
# Go!
trainer.fit()
# Generate video from saved images
if not args.no_ffmpeg:
generate_video(args.save_directory)
log_images_every='never')
##################################################
# Build trainer
from inferno.trainers.basic import Trainer
trainer = Trainer(model)
trainer.build_criterion('CrossEntropyLoss')
trainer.build_metric('CategoricalError')
trainer.build_optimizer('Adam')
trainer.validate_every((2, 'epochs'))
trainer.save_every((5, 'epochs'))
trainer.save_to_directory(SAVE_DIRECTORY)
trainer.set_max_num_epochs(10)
trainer.build_logger(logger, log_directory=LOG_DIRECTORY)
trainer.set_log_directory(LOG_DIRECTORY)
##################################################
# Bind loaders
trainer.bind_loader('train', train_loader)
trainer.bind_loader('validate', validate_loader)
##################################################
from inferno.trainers.callbacks.base import Callback
class SawtoothLearningrate(Callback):
"""oscillating learning rate"""
def __init__(self, min_value, max_value, frequency):
# data loaders
train_loader, validate_loader = get_cifar10_loaders(DATASET_DIRECTORY,
download=DOWNLOAD_CIFAR)
##################################################
# Build trainer
trainer = Trainer(model)
trainer.build_criterion('CrossEntropyLoss')
trainer.build_metric('CategoricalError')
trainer.build_optimizer('Adam')
trainer.validate_every((2, 'epochs'))
trainer.save_every((5, 'epochs'))
trainer.save_to_directory(SAVE_DIRECTORY)
trainer.set_max_num_epochs(10)
trainer.build_logger(TensorboardLogger(log_scalars_every=(1, 'iteration'),
log_images_every='never'),
log_directory=LOG_DIRECTORY)
##################################################
# Bind loaders
trainer.bind_loader('train', train_loader)
trainer.bind_loader('validate', validate_loader)
##################################################
# activate cuda
if USE_CUDA:
trainer.cuda()
##################################################
# fit
trainer.fit()
def set_up_training(project_directory, config):
# Load the model to train from the configuratuib file ('./config/train_config.yml')
model_name = config.get('model_name')
model = getattr(models, model_name)(**config.get('model_kwargs'))
# Initialize the loss: we use the SorensenDiceLoss, which has the nice property
# of being fairly robust for un-balanced targets
criterion = SorensenDiceLoss()
# Wrap the loss to apply additional transformations before the actual
# loss is applied. Here, we apply the mask to the target
# and invert the target (necessary for sorensen dice) during training.
# In addition, we need to remove the segmentation from the target
# during validation (we only keep the segmentation in the target during validation)
loss_train = LossWrapper(criterion=criterion,
transforms=Compose(ApplyAndRemoveMask(),
InvertTarget()))
loss_val = LossWrapper(criterion=criterion,
transforms=Compose(RemoveSegmentationFromTarget(),
ApplyAndRemoveMask(),
InvertTarget()))
# Build the validation metric: we validate by running connected components on
# the affinities for several thresholds
# metric = ArandErrorFromConnectedComponentsOnAffinities(thresholds=[.5, .6, .7, .8, .9],
# invert_affinities=True)
metric = ArandErrorFromConnectedComponents(thresholds=[.5, .6, .7, .8, .9],
invert_input=True,
average_input=True)
logger.info("Building trainer.")
smoothness = 0.95
# Build the trainer object
trainer = Trainer(model)\
.save_every((1000, 'iterations'), to_directory=os.path.join(project_directory, 'Weights'))\
.build_criterion(loss_train)\
.build_validation_criterion(loss_val)\
.build_optimizer(**config.get('training_optimizer_kwargs'))\
.evaluate_metric_every('never')\
.validate_every((100, 'iterations'), for_num_iterations=1)\
.register_callback(SaveAtBestValidationScore(smoothness=smoothness, verbose=True))\
.build_metric(metric)\
.register_callback(AutoLR(factor=0.98,
patience='100 iterations',
monitor_while='validating',
monitor_momentum=smoothness,
consider_improvement_with_respect_to='previous'))
# .register_callback(DumpHDF5Every(frequency='99 iterations',
# to_directory=os.path.join(project_directory, 'debug')))
logger.info("Building logger.")
# Build tensorboard logger
tensorboard = TensorboardLogger(
log_scalars_every=(1, 'iteration'),
log_images_every=(100, 'iterations')).observe_states(
['validation_input', 'validation_prediction, validation_target'],
observe_while='validating')
trainer.build_logger(tensorboard,
log_directory=os.path.join(project_directory, 'Logs'))
return trainer
