def main():
parser = argparse.ArgumentParser()
parser.add_argument("--data_path", type=str, default="data.joblib")
parser.add_argument("--test_strat", type=int, default=0)
parser.add_argument("--device_id", type=int, default=0)
parser.add_argument("--num_epochs_s2cnn", type=int, default=30)
parser.add_argument("--num_epochs_mlp", type=int, default=30)
parser.add_argument("--batch_size_s2cnn", type=int, default=32)
parser.add_argument("--batch_size_mlp", type=int, default=32)
parser.add_argument("--init_learning_rate_s2cnn", type=int, default=1e-3)
parser.add_argument("--learning_rate_mlp", type=int, default=1e-3)
parser.add_argument("--learning_rate_decay_epochs", type=int, default=10)
args = parser.parse_args()
torch.cuda.set_device(args.device_id)
print("evaluating on {}".format(args.test_strat))
print("loading data...", end="")
data, train_idxs, test_idxs = load_data(args.data_path,
args.test_strat,
cuda=args.device_id)
print("done!")
mlp = BaselineRegressor()
s2cnn = S2CNNRegressor()
if torch.cuda.is_available():
for model in [mlp, s2cnn]:
model.cuda(args.device_id)
print("training baseline model")
print("mlp #params: {}".format(count_params(mlp)))
train_baseline(
mlp, data,
IndexBatcher(train_idxs, args.batch_size_mlp, cuda=args.device_id),
IndexBatcher(test_idxs, args.batch_size_mlp, cuda=args.device_id),
args.num_epochs_mlp, args.learning_rate_mlp, args.device_id)
print("training residual s2cnn model")
print("s2cnn #params: {}".format(count_params(s2cnn)))
train_s2cnn(
mlp, s2cnn, data,
IndexBatcher(train_idxs, args.batch_size_s2cnn, cuda=args.device_id),
IndexBatcher(test_idxs, args.batch_size_s2cnn, cuda=args.device_id),
args.num_epochs_s2cnn, args.init_learning_rate_s2cnn,
args.learning_rate_decay_epochs, args.device_id)
def test_conv(Base, nruns=100, device='cuda'):
# will do basic sanity check, we want to get same spatial
# dimension with custom convolutions as in standard module
# to swap convolution types conveniently
chi, cho, k, s = 8, 32, 3, 1
x = torch.randn(16, chi, 512, 512)
conv = Base(chi, cho, k, s, autopad(k))
conv_ = nn.Conv2d(chi, cho, k, s, autopad(k))
if 'cuda' in device:
assert torch.cuda.is_available()
conv.cuda().train()
conv_.cuda().train()
x = x.cuda()
if torch.backends.cudnn.benchmark:
# have to do warm up iterations for fair comparison
print('benchmark warm up...')
for _ in range(50):
_ = conv(x)
else:
conv.cpu().train()
conv_.cpu().train()
nruns = 1
p = count_params(conv)
p_ = count_params(conv_)
# relative number of parameter change in brackets w.r.t. nn.conv2d
print(f'Number of parameters: {p} ({p / p_ * 100:.2f}%)')
# ensure same behaviour as standard module
out = conv(x)
out_ = conv_(x)
assert out.shape == out_.shape, f'Shape missmatch, should be {out_.shape} but is {out.shape}'
# g0 = torch.randn_like(out)
# performance test without feature/target loading
# because that would require a significant amount of overhead
start = time_synchronized()
for _ in range(nruns):
out = conv(x)
for param in conv.parameters():
param.grad = None
out.mean().backward() # out.backward(g0)
end = time_synchronized()
print(f'Forward + Backward time: {(end - start) * 1000 / nruns:.3f}ms')
def test_generator(generator, true_count):
tf.reset_default_graph()
with get_session() as sess:
y = generator(tf.ones((1, 96)), 3)
cur_count = count_params()
if cur_count != true_count:
print(
'Incorrect number of parameters in generator. {0} instead of {1}. Check your achitecture.'
.format(cur_count, true_count))
else:
print('Correct number of parameters in generator.')
x = F.relu(self.sgcn3(x) + self.gcn3d3(x), inplace=True)
x = self.tcn3(x)
out = x
out_channels = out.size(1)
out = out.view(N, M, out_channels, -1)
out = out.mean(3) # Global Average Pooling (Spatial+Temporal)
out = out.mean(1) # Average pool number of bodies in the sequence
out = self.fc(out)
return out
if __name__ == "__main__":
# For debugging purposes
import sys
sys.path.append('..')
model = Model(num_class=60,
num_point=25,
num_person=2,
num_gcn_scales=13,
num_g3d_scales=6,
graph='graph.ntu_rgb_d.AdjMatrixGraph')
N, C, T, V, M = 6, 3, 50, 25, 2
x = torch.randn(N, C, T, V, M)
model.forward(x)
print('Model total # params:', count_params(model))
def build(self):
""" Builds a multi-tower model
"""
with tf.device('/cpu:0'):
assert self.batch_size % self.num_gpus == 0, (
'Batch size must be divisible by number of GPUs')
with tf.name_scope('Input_splits'):
tower_inputs = [[] for i in range(self.num_gpus)]
for inp in self.Inputs:
splits = tf.split(inp, self.num_gpus, name=inp.name[:-2])
for i, s in enumerate(splits):
tower_inputs[i].append(s)
tower_outputs = []
tower_losses = []
tower_grads = []
with tf.variable_scope(tf.get_variable_scope()):
for i in range(self.num_gpus):
with tf.device('/gpu:%d' % i):
with tf.name_scope('%s_%d' % ('tower', i)) as scope:
# Calculate the loss for one tower of the model. This function
# constructs the entire model but shares the variables across
# all towers.
outputs, losses, grads = self._build_train_tower(
tower_inputs[i],
int(self.batch_size / self.num_gpus),
reuse=i > 0 or self.model_built)
# Reuse variables for the next tower.
tf.get_variable_scope().reuse_variables()
# Save summaries from tower_1
if i == 0:
summaries = tf.get_collection(
tf.GraphKeys.SUMMARIES, scope)
tower_outputs.append(outputs)
tower_losses.append(losses)
tower_grads.append(grads)
with tf.name_scope('Concat_outputs'):
outputs = [[] for _ in tower_outputs[0]]
for t_outputs in tower_outputs:
for i, output in enumerate(t_outputs):
outputs[i].append(output)
self.outputs = []
for outs in outputs:
self.outputs.append(tf.concat(outs, 0))
with tf.name_scope('Concat_losses'):
losses = [[] for _ in range(len(tower_losses[0]))]
for t_losses in tower_losses:
for i, loss in enumerate(t_losses):
losses[i].append(loss)
with tf.name_scope('Average_grads'):
var_grads = [[] for _ in range(len(tower_grads[0]))]
for t_grads in tower_grads:
for i, grad in enumerate(t_grads):
var_grads[i].append(grad)
avg_grads = []
for v_grads in var_grads:
avg_grads.append(ops.average_gradients(v_grads))
if self.grad_summ:
# Add histograms for gradients.
with tf.name_scope('Grad_summary'):
grads_summ = []
for var_grads in avg_grads:
for grad, var in var_grads:
if grad is not None:
grads_summ.append(
tf.summary.histogram(
self._remove_tower_name_prefix(var) +
'/Grads', grad))
summaries.append(tf.summary.merge(grads_summ))
if self.var_summ:
# Add histograms for trainable variables.
t_vars = tf.trainable_variables()
with tf.name_scope('Var_summary'):
vars_summ = []
for var in t_vars:
vars_summ.append(
tf.summary.histogram(
self._remove_tower_name_prefix(var), var))
summaries.append(tf.summary.merge(vars_summ))
summaries += self.additional_summaries()
self._tower_outputs(self.outputs)
self._build_train_ops(losses, avg_grads)
self.summary_op = tf.summary.merge(summaries, name='summary_op')
self.saver = tf.train.Saver()
self.model_built = True
utils.count_params()
def main():
args = parse_args()
#args.dataset = "datasets"
if args.name is None:
if args.deepsupervision:
args.name = '%s_%s_wDS' % (args.dataset, args.arch)
else:
args.name = '%s_%s_woDS' % (args.dataset, args.arch)
if not os.path.exists('models/%s' % args.name):
os.makedirs('models/%s' % args.name)
print('Config -----')
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)))
print('------------')
with open('models/%s/args.txt' % args.name, 'w') as f:
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)), file=f)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
# define loss function (criterion)
if args.loss == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[args.loss]().cuda()
cudnn.benchmark = True
# Data loading code
img_paths = glob(
r'D:\Project\CollegeDesign\dataset\Brats2018FoulModel2D\trainImage\*')
mask_paths = glob(
r'D:\Project\CollegeDesign\dataset\Brats2018FoulModel2D\trainMask\*')
train_img_paths, val_img_paths, train_mask_paths, val_mask_paths = \
train_test_split(img_paths, mask_paths, test_size=0.2, random_state=41)
print("train_num:%s" % str(len(train_img_paths)))
print("val_num:%s" % str(len(val_img_paths)))
# create model
print("=> creating model %s" % args.arch)
model = FCN.__dict__[args.arch](args)
model = model.cuda()
print(count_params(model))
if args.optimizer == 'Adam':
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
elif args.optimizer == 'SGD':
optimizer = optim.SGD(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay,
nesterov=args.nesterov)
train_dataset = Dataset(args, train_img_paths, train_mask_paths, args.aug)
val_dataset = Dataset(args, val_img_paths, val_mask_paths)
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
log = pd.DataFrame(
index=[],
columns=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
best_iou = 0
trigger = 0
for epoch in range(args.epochs):
print('Epoch [%d/%d]' % (epoch, args.epochs))
# train for one epoch
train_log = train(args, train_loader, model, criterion, optimizer,
epoch)
# evaluate on validation set
val_log = validate(args, val_loader, model, criterion)
print('loss %.4f - iou %.4f - val_loss %.4f - val_iou %.4f' %
(train_log['loss'], train_log['iou'], val_log['loss'],
val_log['iou']))
tmp = pd.Series(
[
epoch,
args.lr,
train_log['loss'],
train_log['iou'],
val_log['loss'],
val_log['iou'],
],
index=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
log = log.append(tmp, ignore_index=True)
log.to_csv('models/%s/log.csv' % args.name, index=False)
trigger += 1
if val_log['iou'] > best_iou:
torch.save(model.state_dict(), 'models/%s/model.pth' % args.name)
best_iou = val_log['iou']
print("=> saved best model")
trigger = 0
# early stopping
if not args.early_stop is None:
if trigger >= args.early_stop:
print("=> early stopping")
break
torch.cuda.empty_cache()
inverse_model.load_state_dict(torch.load('./models/inverse_model.pth')['model_state_dict'])
model = TandemNet(forward_model, inverse_model)
optimizer = torch.optim.Adam(model.inverse_model.parameters(), lr=configs['learning_rate'], weight_decay=configs['weight_decay'])
elif args.model in ['vae']:
model = cVAE(configs['input_dim'], configs['latent_dim']).to(DEVICE)
optimizer = torch.optim.Adam(model.parameters(), lr=configs['learning_rate'], weight_decay=configs['weight_decay'])
elif args.model in ['gan']:
model = cGAN(configs['input_dim'], configs['output_dim'], configs['noise_dim']).to(DEVICE)
model.apply(weights_init_normal)
optimizer_G = torch.optim.Adam(model.generator.parameters(), lr=configs['g_learning_rate'], weight_decay=configs['weight_decay'])
optimizer_D = torch.optim.Adam(model.discriminator.parameters(), lr=configs['d_learning_rate'], weight_decay=configs['weight_decay'])
print('Model {}, Number of parameters {}'.format(args.model, count_params(model)))
criterion = torch.nn.BCELoss()
trainer = GANTrainer(model, optimizer_G, optimizer_D, train_loader, val_loader, test_loader, criterion, configs['epochs'], args.model)
trainer.fit()
sys.exit(0)
elif args.model in ['inn']:
model = INN(configs['ndim_total'], configs['input_dim'], configs['output_dim'], dim_z = configs['latent_dim']).to(DEVICE)
print('Model {}, Number of parameters {}'.format(args.model, count_params(model)))
optimizer = torch.optim.Adam(model.parameters(), lr=configs['learning_rate'], weight_decay=configs['weight_decay'])
criterion = torch.nn.MSELoss()
trainer = INNTrainer(model, optimizer, train_loader, val_loader, test_loader, criterion, configs['epochs'], args.model)
trainer.fit()
self.outconvm1 = nn.Conv2d(64, out_chan, 1)
def forward(self, x):
x, y1 = self.down1(x)
x, y2 = self.down2(x)
x, y3 = self.down3(x)
x, y4 = self.down4(x)
x = F.dropout2d(F.relu(self.bn1(self.conv1(x))))
x = F.dropout2d(F.relu(self.bn2(self.conv2(x))))
x = self.up4(x, y4)
x = self.up3(x, y3)
x = self.up2(x, y2)
x = self.up1(x, y1)
x1 = self.outconv(x)
return x1
if __name__ == '__main__':
model = Unet(nn.Module)
args = None
# create model
device = 'cpu'
models = model.to(device)
# solution: 1
model = models.cpu()
summary(model, (4, 160, 160))
# print(model)
print(count_params(model))
def main():
parser = argparse.ArgumentParser()
# Model and data are required
parser.add_argument(
"--dir_pretrained_model",
type=str,
required=True,
help=
"Dir containing pre-trained model (checkpoint), which may have been fine-tuned already."
)
# Required for certain modes (--resume, --do_train, --eval_during_training, --do_eval or --do_pred)
parser.add_argument(
"--dir_train",
type=str,
help=
("Dir containing training data (n files named <lang>.train containing unlabeled text)"
))
parser.add_argument(
"--dir_output",
type=str,
help=
"Directory in which model will be written (required if --do_train (but not --resume) or --do_pred)"
)
parser.add_argument(
"--path_dev",
type=str,
help="Path of 2-column TSV file containing labeled validation examples."
)
parser.add_argument(
"--path_test",
type=str,
required=False,
help="Path of text file containing unlabeled test examples.")
# Execution modes
parser.add_argument(
"--resume",
action="store_true",
help=
"Resume training model in --dir_pretrained_model (note: --dir_output will be ignored)"
)
parser.add_argument("--do_train", action="store_true", help="Run training")
parser.add_argument("--eval_during_training",
action="store_true",
help="Run evaluation on dev set during training")
parser.add_argument("--do_eval",
action="store_true",
help="Evaluate model on dev set")
parser.add_argument("--do_pred",
action="store_true",
help="Run prediction on test set")
# Score to optimize on dev set (by early stopping)
parser.add_argument(
"--score_to_optimize",
choices=["track1", "track2", "track3"],
default="track3",
help="Score to optimize on dev set during training (by early stopping)."
)
# Hyperparameters
parser.add_argument(
"--freeze_encoder",
action="store_true",
help=
"Freeze weights of pre-trained encoder. (Note: in this case, we do not keep doing MLM.)"
)
parser.add_argument(
"--no_mlm",
action="store_true",
help=
"Do not keep doing masked language modeling (MLM) during fine-tuning.")
parser.add_argument(
"--sampling_alpha",
type=float,
default=1.0,
help=
"Dampening factor for relative frequencies used to compute language sampling probabilities"
)
parser.add_argument(
"--weight_relevant",
type=float,
default=1.0,
help=
"Relative sampling frequency of relevant languages wrt irrelevant languages"
)
parser.add_argument("--train_batch_size",
default=16,
type=int,
help="Total batch size for training.")
parser.add_argument("--eval_batch_size",
default=64,
type=int,
help="Total batch size for evaluation.")
parser.add_argument(
"--seq_len",
default=128,
type=int,
help=
"Length of input sequences. Shorter seqs are padded, longer ones are trucated"
)
parser.add_argument("--learning_rate",
default=1e-4,
type=float,
help="The initial learning rate for AdamW optimizer.")
parser.add_argument("--equal_betas",
action='store_true',
help="Use beta1=beta2=0.9 for AdamW optimizer.")
parser.add_argument(
"--correct_bias",
action='store_true',
help=
"Correct bias in AdamW optimizer (correct_bias=False is meant to reproduce BERT behaviour exactly."
)
parser.add_argument(
"--max_train_steps",
default=1000000,
type=int,
help=
"Maximum number of training steps to perform. Note: # optimization steps = # train steps / # accumulation steps."
)
parser.add_argument(
"--num_train_steps_per_epoch",
default=1000,
type=int,
help=
"Number of training steps that equals one epoch. Note: # optimization steps = # train steps / # accumulation steps."
)
parser.add_argument(
'--grad_accum_steps',
type=int,
default=1,
help=
"Number of training steps (i.e. batches) to accumualte before performing a backward/update pass."
)
parser.add_argument(
"--num_gpus",
type=int,
default=-1,
help="Num GPUs to use for training (0 for none, -1 for all available)")
parser.add_argument("--local_rank",
type=int,
default=-1,
help="local_rank for distributed training on gpus")
parser.add_argument('--seed',
type=int,
default=42,
help="random seed for initialization")
args = parser.parse_args()
# Distributed or parallel?
if args.local_rank != -1 or args.num_gpus > 1:
raise NotImplementedError(
"No distributed or parallel training available at the moment.")
if torch.cuda.is_available():
args.device = torch.device("cuda")
args.n_gpu = 1
else:
args.device = torch.device("cpu")
args.n_gpu = 0
# Check execution mode
assert args.resume or args.do_train or args.do_eval or args.do_pred
if args.resume:
assert not args.do_train
assert not args.do_eval
assert not args.do_pred
# Load checkpoint. This contains a pre-trained model which may or
# may not have been fine-tuned for language identification already
logger.info("Loading checkpoint...")
checkpoint_path = os.path.join(args.dir_pretrained_model, "checkpoint.tar")
checkpoint_data = torch.load(checkpoint_path)
if args.resume:
# Check progress
logger.info("Resuming training. Currently at training step %d" %
checkpoint_data["global_step"])
# Replace args with initial args for this job, except for
# num_gpus, seed and model directory
current_num_gpus = args.n_gpu
current_dir_pretrained_model = args.dir_pretrained_model
args = deepcopy(checkpoint_data["initial_args"])
args.num_gpus = current_num_gpus
args.dir_pretrained_model = current_dir_pretrained_model
args.resume = True
logger.info("Args (most have been reloaded from checkpoint): %s" %
args)
else:
if args.eval_during_training:
assert args.do_train
if args.do_train or args.do_pred:
assert args.dir_output is not None
if os.path.exists(args.dir_output) and os.path.isdir(
args.dir_output) and len(os.listdir(args.dir_output)) > 1:
msg = "%s already exists and is not empty" % args.dir_output
raise ValueError(msg)
if not os.path.exists(args.dir_output):
os.makedirs(args.dir_output)
if args.do_train:
assert args.dir_train is not None
train_paths = glob.glob(os.path.join(args.dir_train, "*.train"))
assert len(train_paths) > 0
checkpoint_data["initial_args"] = args
if args.do_train and args.freeze_encoder and not args.no_mlm:
logger.warning(
"Setting --no_mlm to True since --freeze_encoder is True, therefore doing MLM would be pointless."
)
args.no_mlm = True
if args.do_eval or args.eval_during_training:
assert args.path_dev is not None
assert os.path.exists(args.path_dev)
if args.do_pred:
assert args.path_test is not None
assert os.path.exists(args.path_test)
if args.grad_accum_steps < 1:
raise ValueError(
"Invalid grad_accum_steps parameter: {}, should be >= 1".format(
args.grad_accum_steps))
# Create list of languages we handle
lang_list = sorted(ALL_LANGS)
# Seed RNGs
np.random.seed(args.seed)
torch.manual_seed(args.seed)
if args.n_gpu > 0:
torch.cuda.manual_seed_all(args.seed)
# Load tokenizer
logger.info("Loading tokenizer...")
tokenizer_path = os.path.join(args.dir_pretrained_model, "tokenizer.pkl")
with open(tokenizer_path, "rb") as f:
tokenizer = pickle.load(f)
# Make encoder and model
logger.info("Making encoder...")
encoder_config = BertConfig.from_json_file(
os.path.join(args.dir_pretrained_model, "config.json"))
encoder = BertForMaskedLM(encoder_config)
logger.info("Making model...")
model = BertForLangID(encoder, lang_list)
model.to(args.device)
# Load model weights. First, check if we just have an encoder, or a previously fine-tuned model
if "classifier.dense.weight" in checkpoint_data["model_state_dict"]:
if "best_model_state_dict" in checkpoint_data and not args.resume:
logger.info("Loading model weights from 'best_model_state_dict'")
model.load_state_dict(checkpoint_data["best_model_state_dict"])
else:
logger.info("Loading model weights from 'model_state_dict'")
model.load_state_dict(checkpoint_data["model_state_dict"])
else:
# Model has not previously been fine-tuned, so we only load encoder weights
assert args.do_train
logger.info("Loading encoder weights from 'model_state_dict'")
model.encoder.load_state_dict(checkpoint_data["model_state_dict"])
if (args.do_train or args.resume) and args.freeze_encoder:
model.freeze_encoder()
# Write encoder config and tokenizer in output directory
if (not args.resume) and args.do_train:
path_config = os.path.join(args.dir_output, "config.json")
model.encoder.config.to_json_file(path_config)
path_tokenizer = os.path.join(args.dir_output, "tokenizer.pkl")
with open(path_tokenizer, "wb") as f:
pickle.dump(tokenizer, f)
# Log some info on the model
logger.info("Encoder config: %s" % repr(model.encoder.config))
logger.info("Model params:")
for n, p in model.named_parameters():
msg = " %s" % n
if not p.requires_grad:
msg += " ***FROZEN***"
logger.info(msg)
logger.info("Nb model params: %d" % count_params(model))
logger.info("Nb params in encoder: %d" % count_params(model.encoder))
logger.info("Nb params in pooler: %d" % count_params(model.pooler))
logger.info("Nb params in classifier: %d" % count_params(model.classifier))
# Get data
max_seq_length = args.seq_len + 2 # We add 2 for CLS and SEP
if args.resume:
# Reload training dataset(s)
logger.info("Reloading training data from checkpoint")
train_dataset = checkpoint_data["train_dataset"]
train_dataset.prep_files_for_streaming()
dev_dataset = checkpoint_data.get("dev_dataset", None)
unk_dataset = checkpoint_data.get("unk_dataset", None)
if unk_dataset:
unk_dataset.prep_files_for_streaming()
elif args.do_train:
# Remove unk.train if present, and create a MLM dataset for it.
path_unk = check_for_unk_train_data(train_paths)
if path_unk is None:
unk_dataset = None
else:
train_paths.remove(path_unk)
logger.info("Creating MLM-only training set from %s..." % path_unk)
unk_dataset = BertDatasetForMLM(
[path_unk],
tokenizer,
max_seq_length,
sampling_alpha=args.sampling_alpha,
weight_relevant=args.weight_relevant,
encoding="utf-8",
seed=args.seed,
verbose=DEBUG)
logger.info("Creating training set from %s training files in %s..." %
(len(train_paths), args.dir_train))
train_dataset = BertDatasetForClassification(
train_paths,
tokenizer,
max_seq_length,
include_mlm=True,
sampling_alpha=args.sampling_alpha,
weight_relevant=args.weight_relevant,
encoding="utf-8",
seed=args.seed,
verbose=DEBUG)
if path_unk is not None:
assert len(unk_dataset) == len(train_dataset)
# Check train_dataset.lang2id: keys should contain all langs, and nothing else, like that of the model
assert train_dataset.lang2id == model.lang2id
if not args.resume:
dev_dataset = None
if args.do_eval or args.eval_during_training:
logger.info("Loading validation data from %s..." % args.path_dev)
dev_dataset = BertDatasetForTesting(args.path_dev,
tokenizer,
model.lang2id,
max_seq_length,
require_labels=True,
encoding="utf-8",
verbose=DEBUG)
if args.do_train and args.eval_during_training:
checkpoint_data["dev_dataset"] = dev_dataset
if args.do_pred:
logger.info("Loading test data from %s..." % args.path_test)
test_dataset = BertDatasetForTesting(args.path_test,
tokenizer,
model.lang2id,
max_seq_length,
require_labels=False,
encoding="utf-8",
verbose=DEBUG)
# Compute number of epochs and steps, initialize number of training steps done.
num_opt_steps_per_epoch = args.num_train_steps_per_epoch // args.grad_accum_steps
args.num_epochs = math.ceil(checkpoint_data["max_opt_steps"] /
num_opt_steps_per_epoch)
if args.do_train and (not args.resume):
checkpoint_data["global_step"] = 0
checkpoint_data[
"max_opt_steps"] = args.max_train_steps // args.grad_accum_steps
# Training
if args.do_train or args.resume:
# Prepare optimizer
logger.info("Preparing optimizer...")
np_list = list(model.named_parameters())
no_decay = ['bias', 'LayerNorm.bias', 'LayerNorm.weight']
opt_params = [{
'params':
[p for n, p in np_list if not any(nd in n for nd in no_decay)],
'weight_decay':
0.01
}, {
'params':
[p for n, p in np_list if any(nd in n for nd in no_decay)],
'weight_decay':
0.0
}]
if args.equal_betas:
betas = (0.9, 0.9)
else:
betas = (0.9, 0.999)
optimizer = AdamW(
opt_params,
lr=args.learning_rate,
betas=betas,
correct_bias=args.correct_bias
) # To reproduce BertAdam specific behaviour, use correct_bias=False
# Load optimizer state if resuming
if args.resume:
optimizer.load_state_dict(checkpoint_data["optimizer_state_dict"])
# Log some info before training
logger.info("*** Training info: ***")
logger.info(" Number of training steps completed: %d" %
checkpoint_data["global_step"])
logger.info(" Max training steps: %d" % args.max_train_steps)
logger.info(" Gradient accumulation steps: %d" %
args.grad_accum_steps)
logger.info(" Max optimization steps: %d" %
checkpoint_data["max_opt_steps"])
logger.info(" Training dataset size: %d" % len(train_dataset))
logger.info(" Batch size: %d" % args.train_batch_size)
logger.info(" # training steps/epoch: %d" %
(args.num_train_steps_per_epoch))
logger.info(" # optimization steps/epoch: %d" %
num_opt_steps_per_epoch)
logger.info(" # epochs to do: %d" % args.num_epochs)
if args.eval_during_training:
logger.info("Validation dataset size: %d" % len(dev_dataset))
# Run training
train(model,
optimizer,
train_dataset,
args,
checkpoint_data,
dev_dataset=dev_dataset,
unk_dataset=unk_dataset)
# Reload model
save_to_dir = args.dir_pretrained_model if args.resume else args.dir_output
checkpoint_data = torch.load(
os.path.join(save_to_dir, "checkpoint.tar"))
if "best_model_state_dict" in checkpoint_data:
model.load_state_dict(checkpoint_data["best_model_state_dict"])
else:
model.load_state_dict(checkpoint_data["model_state_dict"])
# Evaluate model on dev set
if args.do_eval:
logger.info("*** Running evaluation... ***")
scores = evaluate(model, dev_dataset, args)
logger.info("***** Evaluation Results *****")
for score_name in sorted(scores.keys()):
logger.info("- %s: %.4f" % (score_name, scores[score_name]))
# Get model's predictions on test set
if args.do_pred:
logger.info("*** Running prediction... ***")
logits = predict(model, test_dataset, args)
pred_class_ids = np.argmax(logits.cpu().numpy(), axis=1)
pred_labels = [test_dataset.label_list[i] for i in pred_class_ids]
path_pred = os.path.join(args.dir_output, "pred.txt")
logger.info("Writing predictions in %s..." % path_pred)
with open(path_pred, 'w', encoding="utf-8") as f:
for x in pred_labels:
f.write("%s\n" % x)
def run(self):
# load data
args_dict = self._default_configs()
args = dotdict(args_dict)
feature_dirs, label_dirs = get_data(datadir, level, train_dataset,
dev_dataset, test_dataset, mode)
batchedData, maxTimeSteps, totalN = self.load_data(
feature_dirs[0], label_dirs[0], mode, level)
model = model_fn(args, maxTimeSteps)
FL_pair = list(zip(feature_dirs, label_dirs))
random.shuffle(FL_pair)
feature_dirs, label_dirs = zip(*FL_pair)
print("Feature dirs:", feature_dirs)
for feature_dir, label_dir in zip(feature_dirs, label_dirs):
id_dir = feature_dirs.index(feature_dir)
print('dir id:{}'.format(id_dir))
batchedData, maxTimeSteps, totalN = self.load_data(
feature_dir, label_dir, mode, level)
model = model_fn(args, maxTimeSteps)
num_params = count_params(model, mode='trainable')
all_num_params = count_params(model, mode='all')
model.config['trainable params'] = num_params
model.config['all params'] = all_num_params
print(model.config)
with tf.Session(graph=model.graph) as sess:
# restore from stored model
if keep == True:
ckpt = tf.train.get_checkpoint_state(savedir)
if ckpt and ckpt.model_checkpoint_path:
model.saver.restore(sess, ckpt.model_checkpoint_path)
print('Model restored from:' + savedir)
else:
print('Initializing')
sess.run(model.initial_op)
total_cont = 0
for epoch in range(num_epochs):
## training
start = time.time()
if mode == 'train':
print('Epoch {} ...'.format(epoch + 1))
batchErrors = np.zeros(len(batchedData))
batchRandIxs = np.random.permutation(len(batchedData))
for batch, batchOrigI in enumerate(batchRandIxs):
batchInputs, batchTargetSparse, batchSeqLengths = batchedData[
batchOrigI]
batchTargetIxs, batchTargetVals, batchTargetShape = batchTargetSparse
feedDict = {
model.inputX: batchInputs,
model.targetIxs: batchTargetIxs,
model.targetVals: batchTargetVals,
model.targetShape: batchTargetShape,
model.seqLengths: batchSeqLengths
}
_, l, pre, y, er = sess.run([
model.optimizer, model.loss, model.predictions,
model.targetY, model.errorRate
],
feed_dict=feedDict)
batchErrors[batch] = er
print(
'\n{} mode, total:{},subdir:{}/{},batch:{}/{},epoch:{}/{},train loss={:.3f},mean train CER={:.3f}\n'
.format(level, totalN, id_dir + 1,
len(feature_dirs), batch + 1,
len(batchRandIxs), epoch + 1, num_epochs,
l, er / batch_size))
total_cont += 1
if batch % 20 == 0:
print('Truth:\n' +
output_to_sequence(y, type=level))
print('Output:\n' +
output_to_sequence(pre, type=level))
checkpoint_path = os.path.join(
savedir, 'model.ckpt')
model.saver.save(sess,
checkpoint_path,
global_step=total_cont)
print('Model has been saved in {}'.format(savedir))
end = time.time()
delta_time = end - start
print('Epoch ' + str(epoch + 1) + ' needs time:' +
str(delta_time) + ' s')
def train(self, args):
''' import data, train model, save model
'''
text_parser = TextParser(args.data_dir, args.batch_size,
args.seq_length)
args.vocab_size = text_parser.vocab_size
ckpt = tf.train.get_checkpoint_state(args.save_dir)
if args.keep is True:
# check if all necessary files exist
if os.path.exists(os.path.join(args.save_dir,'config.pkl')) and \
os.path.exists(os.path.join(args.save_dir,'words_vocab.pkl')) and \
ckpt and ckpt.model_checkpoint_path:
with open(os.path.join(args.save_dir, 'config.pkl'),
'rb') as f:
saved_model_args = cPickle.load(f)
with open(os.path.join(args.save_dir, 'words_vocab.pkl'),
'rb') as f:
saved_words, saved_vocab = cPickle.load(f)
else:
raise ValueError('configuration doesn"t exist!')
if args.model == 'seq2seq_rnn':
model = Model_rnn(args)
else:
# TO ADD OTHER MODEL
pass
trainable_num_params = count_params(model, mode='trainable')
all_num_params = count_params(model, mode='all')
args.num_trainable_params = trainable_num_params
args.num_all_params = all_num_params
print(args.num_trainable_params)
print(args.num_all_params)
with open(os.path.join(args.save_dir, 'config.pkl'), 'wb') as f:
cPickle.dump(args, f)
with open(os.path.join(args.save_dir, 'words_vocab.pkl'), 'wb') as f:
cPickle.dump((text_parser.vocab_dict, text_parser.vocab_list), f)
with tf.Session() as sess:
if args.keep is True:
print('Restoring')
model.saver.restore(sess, ckpt.model_checkpoint_path)
else:
print('Initializing')
sess.run(model.initial_op)
for e in range(args.num_epochs):
start = time.time()
#sess.run(tf.assign(model.lr, args.learning_rate * (args.decay_rate ** e)))
sess.run(tf.assign(model.lr, args.learning_rate))
model.initial_state = tf.convert_to_tensor(model.initial_state)
state = model.initial_state.eval()
total_loss = []
for b in range(text_parser.num_batches):
x, y = text_parser.next_batch()
print('flag')
feed = {
model.input_data: x,
model.targets: y,
model.initial_state: state
}
train_loss, state, _ = sess.run(
[model.cost, model.final_state, model.train_op], feed)
total_loss.append(train_loss)
print("{}/{} (epoch {}), train_loss = {:.3f}" \
.format(e * text_parser.num_batches + b, \
args.num_epochs * text_parser.num_batches, \
e, train_loss))
if (e * text_parser.num_batches +
b) % args.save_every == 0 or (
e == args.num_epochs - 1
and b == text_parser.num_batches - 1):
checkpoint_path = os.path.join(args.save_dir,
'model.ckpt')
model.saver.save(sess, checkpoint_path, global_step=e)
print("model has been saved in:" +
str(checkpoint_path))
end = time.time()
delta_time = end - start
ave_loss = np.array(total_loss).mean()
logging(model, ave_loss, e, delta_time, mode='train')
if ave_loss < 0.5:
break
def main():
args = parse_args()
# add model name to args
if args.name is None:
args.name = '%s_%s' % (args.arch, datetime.now().strftime('%m%d%H%M'))
if not os.path.exists('models/%s' % args.name):
os.makedirs('models/%s' % args.name)
print('Config -----')
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)))
print('------------')
with open('models/%s/args.txt' % args.name, 'w') as f:
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)), file=f)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
if args.seed is not None:
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
cudnn.deterministic = True
warnings.warn('You have chosen to seed training. '
'This will turn on the CUDNN deterministic setting, '
'which can slow down your training considerably! '
'You may see unexpected behavior when restarting '
'from checkpoints.')
if args.gpu is not None:
warnings.warn('You have chosen a specific GPU. This will completely '
'disable data parallelism.')
# define loss function (criterion)
if args.loss == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda(args.gpu)
else:
criterion = losses.__dict__[args.loss]().cuda(args.gpu)
cudnn.benchmark = True
# Data loading code
train_df = pd.read_csv('input/train.csv')
img_paths = 'input/train/images/' + train_df['id'].values + '.png'
mask_paths = 'input/train/masks/' + train_df['id'].values + '.png'
if args.cv == 'KFold':
kf = KFold(n_splits=args.n_splits, shuffle=True, random_state=41)
cv = kf.split(img_paths)
elif args.cv == 'Cov':
train_df['cov'] = 0
for i in tqdm(range(len(train_df))):
mask = imread('input/train/masks/' + train_df['id'][i] + '.png')
mask = mask.astype('float32') / 255
train_df.loc[i, 'cov'] = ((np.sum(mask > 0.5) / 101**2) *
10).astype('int')
skf = StratifiedKFold(n_splits=args.n_splits,
shuffle=True,
random_state=41)
cv = skf.split(img_paths, train_df['cov'])
for fold, (train_idx, val_idx) in enumerate(cv):
print('Fold [%d/%d]' % (fold + 1, args.n_splits))
# create model
print("=> creating model %s (pretrained=%s)" %
(args.arch, str(args.pretrained)))
model = archs.__dict__[args.arch](args)
if args.freeze_bn:
model.freeze_bn()
if args.gpu is not None:
model = model.cuda(args.gpu)
else:
model = torch.nn.DataParallel(model).cuda()
print(count_params(model))
if args.optimizer == 'Adam':
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
elif args.optimizer == 'SGD':
optimizer = optim.SGD(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay,
nesterov=args.nesterov)
if args.scheduler == 'MultiStepLR':
if args.reduce_epoch is None:
scheduler = lr_scheduler.MultiStepLR(optimizer,
milestones=[],
gamma=0.1)
else:
scheduler = lr_scheduler.MultiStepLR(
optimizer, milestones=[args.reduce_epoch], gamma=0.1)
elif args.scheduler == 'CyclicLR':
scheduler = CyclicLR(optimizer, step_size=800)
elif args.scheduler == 'CosineAnnealingLR':
scheduler = lr_scheduler.CosineAnnealingLR(optimizer,
T_max=args.epochs,
eta_min=args.min_lr)
elif args.scheduler == 'StepLR':
scheduler = lr_scheduler.StepLR(optimizer, 20, gamma=0.5)
train_img_paths, val_img_paths = img_paths[train_idx], img_paths[
val_idx]
train_mask_paths, val_mask_paths = mask_paths[train_idx], mask_paths[
val_idx]
train_dataset = Dataset(args, train_img_paths, train_mask_paths)
val_dataset = Dataset(args, val_img_paths, val_mask_paths, False)
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
log = pd.DataFrame(
index=[],
columns=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
best_loss = float('inf')
trigger = 0
for epoch in range(args.epochs):
if args.scheduler == 'CyclicLR':
# train for one epoch
train_log = train(args, train_loader, model, criterion,
optimizer, epoch, scheduler)
else:
scheduler.step()
# train for one epoch
train_log = train(args, train_loader, model, criterion,
optimizer, epoch)
# evaluate on validation set
val_log = validate(args, val_loader, model, criterion)
tmp = pd.Series(
[
epoch,
scheduler.get_lr()[0],
train_log['loss'],
train_log['iou'],
val_log['loss'],
val_log['iou'],
],
index=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
log = log.append(tmp, ignore_index=True)
log.to_csv('models/%s/log_%d.csv' % (args.name, fold + 1),
index=False)
trigger += 1
if val_log['loss'] < best_loss:
torch.save(model.state_dict(),
'models/%s/model_%d.pth' % (args.name, fold + 1))
best_loss = val_log['loss']
print("=> saved best model")
trigger = 0
# early stopping
if not args.early_stop is None:
if epoch > args.epochs * 0.8 and trigger >= args.early_stop:
print("=> early stopping")
break
torch.cuda.empty_cache()
def run(self):
# load data
args_dict = self._default_configs()
args = dotdict(args_dict) # 创建dotdict类，类似创造自己的dict
feature_dirs, label_dirs = get_data(datadir, level, train_dataset,
dev_dataset, test_dataset, mode)
# batchedData, maxTimeSteps, totalN = self.load_data(feature_dirs[0], label_dirs[0], mode, level)
# model = model_fn(args, maxTimeSteps)
# # 此两行作用不明白，删掉后不知道有什么影响
# 记录每次epoch的
# shuffle feature_dir and label_dir by same order
FL_pair = list(zip(feature_dirs,
label_dirs)) # zip()后返回特定zip数据？，list让其变成列表
random.shuffle(FL_pair) # 打乱列表中元素顺序
feature_dirs, label_dirs = zip(*FL_pair)
for feature_dir, label_dir in zip(
feature_dirs, label_dirs): # zip()返回结果可用于for, 展示时用list()展出
id_dir = feature_dirs.index(feature_dir)
print('dir id:{}'.format(id_dir))
batchedData, maxTimeSteps, totalN = self.load_data(
feature_dir, label_dir, mode, level)
model = model_fn(args, maxTimeSteps) # 建立神经网络的图
num_params = count_params(model, mode='trainable')
all_num_params = count_params(model, mode='all')
model.config['trainable params'] = num_params
model.config['all params'] = all_num_params
print(model.config)
with tf.Session(graph=model.graph, config=config) as sess:
# restore from stored model
if keep: # 用于重新训练 keep == True
ckpt = tf.train.get_checkpoint_state(savedir)
# Returns CheckpointState proto from the "checkpoint" file.
if ckpt and ckpt.model_checkpoint_path: # The checkpoint file
model.saver.restore(sess, ckpt.model_checkpoint_path)
print('Model restored from:' + savedir)
else:
print('Initializing')
sess.run(model.initial_op)
for step in range(num_steps):
# training
start = time.time()
if mode == 'train':
print('step {} ...'.format(step + 1))
batchErrors = np.zeros(len(batchedData))
batchRandIxs = np.random.permutation(len(batchedData))
# 如果传给permutation一个矩阵，它会返回一个洗牌后的矩阵副本
for batch, batchOrigI in enumerate(batchRandIxs):
# 对于一个可迭代的（iterable）/可遍历的对象（如列表、字符串），enumerate将其组成一个索引序列，
# 利用它可以同时获得索引和值 这部分代码用于feed_Dict
batchInputs, batchTargetSparse, batchSeqLengths = batchedData[
batchOrigI]
batchTargetIxs, batchTargetVals, batchTargetShape = batchTargetSparse
feedDict = {
model.inputX: batchInputs,
model.targetIxs: batchTargetIxs,
model.targetVals: batchTargetVals,
model.targetShape: batchTargetShape,
model.seqLengths: batchSeqLengths
}
if level == 'cha':
if mode == 'train':
_, l, pre, y, er = sess.run([
model.optimizer, model.loss,
model.predictions, model.targetY,
model.errorRate
],
feed_dict=feedDict)
batchErrors[
batch] = er # batchError 207 batch 211
print(
'\n{} mode, total:{},subdir:{}/{},batch:{}/{},step:{},train loss={:.3f},mean '
'train CER={:.3f}, epoch: {}\n'.format(
level, totalN, id_dir + 1,
len(feature_dirs), batch + 1,
len(batchRandIxs), step + 1, l,
er / batch_size, num_epochs))
elif mode == 'dev':
l, pre, y, er = sess.run([
model.loss, model.predictions,
model.targetY, model.errorRate
],
feed_dict=feedDict)
batchErrors[batch] = er
print(
'\n{} mode, total:{},subdir:{}/{},batch:{}/{},dev loss={:.3f},'
'mean dev CER={:.3f}\n'.format(
level, totalN, id_dir + 1,
len(feature_dirs), batch + 1,
len(batchRandIxs), l, er / batch_size))
elif mode == 'test':
l, pre, y, er = sess.run([
model.loss, model.predictions,
model.targetY, model.errorRate
],
feed_dict=feedDict)
batchErrors[batch] = er
print(
'\n{} mode, total:{},subdir:{}/{},batch:{}/{},test loss={:.3f},'
'mean test CER={:.3f}\n'.format(
level, totalN, id_dir + 1,
len(feature_dirs), batch + 1,
len(batchRandIxs), l, er / batch_size))
elif level == 'seq2seq':
raise ValueError('level %s is not supported now' %
str(level))
# NOTE: ??????for what
# if er / batch_size == 1.0:
# break
if batch % 20 == 0:
print('Truth:\n' +
output_to_sequence(y, type=level))
print('Output:\n' +
output_to_sequence(pre, type=level))
if mode == 'train' and (
(step * len(batchRandIxs) + batch + 1) % 20 == 0 or
(step == num_steps - 1
and batch == len(batchRandIxs) - 1)):
# 每当算式结果是20倍数 或者 跑完一个 subdir的 batch后， 记录model
checkpoint_path = os.path.join(
savedir, 'model.ckpt')
model.saver.save(sess,
checkpoint_path,
global_step=step)
print('Model has been saved in {}'.format(savedir))
end = time.time()
delta_time = end - start
print('subdir ' + str(id_dir + 1) + ' needs time:' +
str(delta_time) + ' s')
if mode == 'train':
if (step + 1) % 1 == 0:
checkpoint_path = os.path.join(
savedir, 'model.ckpt')
model.saver.save(sess,
checkpoint_path,
global_step=step)
print('Model has been saved in {}'.format(savedir))
epochER = batchErrors.sum() / totalN
print('subdir', id_dir + 1, 'mean train error rate:',
epochER) # 修改epoch成subdir
logging(model,
logfile,
epochER,
id_dir,
delta_time,
mode='config')
logging(model,
logfile,
epochER,
id_dir,
delta_time,
mode=mode)
if mode == 'test' or mode == 'dev':
with open(
os.path.join(resultdir, level + '_result.txt'),
'a') as result:
result.write(
output_to_sequence(y, type=level) + '\n')
result.write(
output_to_sequence(pre, type=level) + '\n')
result.write('\n')
epochER = batchErrors.sum() / totalN
print(' test error rate:', epochER)
logging(model, logfile, epochER, mode=mode)
def main():
args = parse_args()
if args.name is None:
if args.deepsupervision:
args.name = '%s_%s_wDS' % (args.dataset, args.arch)
else:
args.name = '%s_%s_woDS' % (args.dataset, args.arch)
if not os.path.exists('models/%s' % args.name):
os.makedirs('models/%s' % args.name)
writer = SummaryWriter('models/%s/test' % args.name)
print('Config -----')
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)))
print('------------')
with open('models/%s/args.txt' % args.name, 'w') as f:
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)), file=f)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
# define loss function (criterion)
if args.loss == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[args.loss]().cuda()
cudnn.benchmark = True
# Data loading code
img_paths = glob('input/' + args.dataset + '/images/*')
mask_paths = glob('input/' + args.dataset + '/masks/*')
train_img_paths, val_img_paths, train_mask_paths, val_mask_paths = \
train_test_split(img_paths, mask_paths, test_size=0.2, random_state=41)
# create model
print("=> creating model %s" % args.arch)
model = archs.__dict__[args.arch](args)
model = model.cuda()
# print(type(model))
######## model visualization in tensorboard ##############
dummy_input = torch.rand(1, 3, 256, 256).cuda()
writer.add_graph(model, (dummy_input, ))
print(count_params(model))
if args.optimizer == 'Adam':
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
elif args.optimizer == 'SGD':
optimizer = optim.SGD(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay,
nesterov=args.nesterov)
train_dataset = Dataset(args, train_img_paths, train_mask_paths, args.aug)
val_dataset = Dataset(args, val_img_paths, val_mask_paths)
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
log = pd.DataFrame(
index=[],
columns=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
best_iou = 0
trigger = 0
for epoch in range(args.epochs):
print('Epoch [%d/%d]' % (epoch, args.epochs))
# changing lr
adjust_learning_rate(args, optimizer, epoch, writer)
# optimizer
# train for one epoch
train_log = train(args, train_loader, model, criterion, optimizer,
epoch)
# evaluate on validation set
val_log = validate(args, val_loader, model, criterion)
print('loss %.4f - iou %.4f - val_loss %.4f - val_iou %.4f' %
(train_log['loss'], train_log['iou'], val_log['loss'],
val_log['iou']))
# vis in tensorboard
writer.add_scalar('train_loss', train_log['loss'], epoch)
writer.add_scalar('train_iou', train_log['iou'], epoch)
writer.add_scalar('val_loss', val_log['loss'], epoch)
writer.add_scalar('val_iou', val_log['iou'], epoch)
tmp = pd.Series(
[
epoch,
args.lr,
train_log['loss'],
train_log['iou'],
val_log['loss'],
val_log['iou'],
],
index=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
log = log.append(tmp, ignore_index=True)
log.to_csv('models/%s/log.csv' % args.name, index=False)
trigger += 1
if val_log['iou'] > best_iou:
torch.save(model.state_dict(), 'models/%s/model.pth' % args.name)
best_iou = val_log['iou']
print("=> saved best model")
trigger = 0
#todo: save model with best dice
# early stopping
if not args.early_stop is None:
if trigger >= args.early_stop:
print("=> early stopping")
break
torch.cuda.empty_cache()
CHAR_EMBEDDING_MATRIX = model.add_lookup_parameters(
(num_chars, char_embedding_size))
word_lstm = dy.LSTMBuilder(num_layers, embedding_size, lstm_out, model)
char_fw_lstm = dy.LSTMBuilder(1, char_embedding_size, char_lstm_out, model)
char_bw_lstm = dy.LSTMBuilder(1, char_embedding_size, char_lstm_out, model)
softmax_w = model.add_parameters((num_words, lstm_out))
softmax_b = model.add_parameters((num_words))
params = [CHAR_EMBEDDING_MATRIX, softmax_w, softmax_b]
params.extend(*word_lstm.get_parameters())
params.extend(*char_fw_lstm.get_parameters())
params.extend(*char_bw_lstm.get_parameters())
print("Number of Params: {}".format(count_params(params)))
def word_rep(word, fw_init, bw_init):
pad = char_vocab.get('<*>')
indices = [pad] + [char_vocab.get(c) for c in word] + [pad]
embedded = [CHAR_EMBEDDING_MATRIX[i] for i in indices]
forward = fw_init.transduce(embedded)
backward = bw_init.transduce(embedded)
return dy.concatenate([forward[-1], backward[-1]])
def calc_lm_loss(words):
dy.renew_cg()
sm_w = dy.parameter(softmax_w)
def evaluate(SMASH, which_dataset, batch_size, seed, validate, num_random,
num_perturb, num_markov, perturb_prob, arch_SGD, fp16, parallel):
# Random seeds
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
np.random.seed(seed)
num_runs = num_random + num_perturb + num_markov
random_sample = True
perturb = False
markov = False
net = torch.load('weights/' + SMASH + '.pth')
net.eval()
# Backwards compatibility hack; If you're trying to understand this code,
# ignore this line.
if not hasattr(net, 'factors'):
net.factors = factors(net.N)
_, test_loader = get_data_loader(which_dataset=which_dataset,
augment=False,
validate=validate,
batch_size=batch_size)
# Prepare lists that hold errors
ensemble_err, err, flops, params = [], [], [], []
# Array to which we save configurations and errors
save_archs = []
# Prepare ensemble predictions
ensemble_out = torch.zeros(len(test_loader.dataset),
net.fc.out_features).cuda()
# Start the stopwatch and begin testing
start_time = time.time()
mode = 'training' if net.training else 'testing'
print('Evaluating %s in %s mode...' % (SMASH, mode))
for test in range(num_runs):
# If we've done all our random samples, switch to random perturbation mode
if test == num_random:
sorted_archs = sorted(save_archs, key=lambda item: item[-1])
print(
'Random sampling complete with best error of %f, starting perturbation...'
% (sorted_archs[0][-1]))
base_arch = sorted_archs[0][:10]
perturb = True
random_sample = False
# If we've done all our perturbations, switch to markov chain mode
elif test == num_random + num_perturb:
sorted_archs = sorted(save_archs, key=lambda item: item[-1])
print(
'Random perturbation complete with best error of %f, starting markov chain...'
% (sorted_archs[0][-1]))
base_arch = sorted_archs[0][:10]
current_error = sorted_archs[0][-1]
markov = True
# Sample a random architecture, as in training
if random_sample:
arch = net.sample_architecture()
# Slightly change a sampled (and, presumably, high-scoring) architecture
elif perturb:
arch = perturb_arch.perturb_architecture(net, deepcopy(base_arch),
perturb_prob)
#Sample Weights
w1x1 = net.sample_weights(*arch)
# Error counters
e, ensemble_e = 0, 0
# Loop over validation set
for i, (x, y) in enumerate(test_loader):
# Get outputs
o = net(V(x.cuda(), volatile=True), w1x1, *arch)
# Get predictions ensembled across multiple configurations
ensemble_out[i * batch_size:(i + 1) * batch_size] += o.data
# Update error
e += o.data.max(1)[1].cpu().ne(y).sum()
# Update ensemble error
ensemble_e += ensemble_out[i * batch_size:(i + 1) *
batch_size].max(1)[1].cpu().ne(y).sum()
# Save ensemble error thus far
ensemble_err.append(float(ensemble_e) / ensemble_out.size(0))
# Save individual error thus far
err.append(float(e) / ensemble_out.size(0))
# While in markov mode, update the base arch if we get a better SMAS hscore.
if markov and err[-1] < float(current_error):
print(
'Error of %f superior to error of %f, accepting new architecture...'
% (err[-1], current_error))
base_arch = arch
current_error = err[-1]
# Save relevant architectural details along with error
save_archs.append(arch +
(net.N, net.N_max, net.bottleneck,
net.max_bottleneck, net.in_channels, 0, err[-1]))
params.append(count_params(save_archs[-1]))
flops.append(count_flops(save_archs[-1], which_dataset))
print(
'For run #%d/%d, Individual Error %2.2f Ensemble Err %2.2f, params %e, flops %e, Time Elapsed %d.'
% (test, num_runs, 100 * err[-1], 100 * ensemble_err[-1],
params[-1], flops[-1], time.time() - start_time)
) #LogSof EnsErr %d, Softmax EnsErr %d ensemble_olgs_err[-1], ensemble_os_err[-1],
best_acc = sorted(err)[0]
worst_acc = sorted(err)[-1]
least_flops = sorted(flops)[0]
most_flops = sorted(flops)[-1]
least_params = sorted(params)[0]
most_params = sorted(params)[-1]
print('Best accuracy is ' + str(best_acc) + ', Worst accuracy is ' +
str(worst_acc))
# Save results
# np.savez(filename[:-4] + '_' + mode + '_errors.npz', **{'err':err, 'ensemble_err':ensemble_err})
# save_archs = sorted(save_archs, key = lambda item: item[-1])
np.savez(
SMASH + '_archs.npz', **{
'archs': sorted(save_archs, key=lambda item: item[-1]),
'unsorted_archs': save_archs
})
def __init__(self, model, vocab):
assert isinstance(model, dict) or isinstance(model, str)
assert isinstance(vocab, tuple) or isinstance(vocab, str)
# dataset
logger.info('-' * 100)
logger.info('Loading training and validation dataset')
self.dataset = data.CodePtrDataset(mode='test')
self.dataset_size = len(self.dataset)
logger.info('Size of training dataset: {}'.format(self.dataset_size))
logger.info('The dataset are successfully loaded')
self.dataloader = DataLoader(dataset=self.dataset,
batch_size=config.test_batch_size,
collate_fn=lambda *args: utils.collate_fn(args,
source_vocab=self.source_vocab,
code_vocab=self.code_vocab,
ast_vocab=self.ast_vocab,
nl_vocab=self.nl_vocab,
raw_nl=True))
# vocab
logger.info('-' * 100)
if isinstance(vocab, tuple):
logger.info('Vocabularies are passed from parameters')
assert len(vocab) == 4
self.source_vocab, self.code_vocab, self.ast_vocab, self.nl_vocab = vocab
else:
logger.info('Vocabularies are read from dir: {}'.format(vocab))
self.source_vocab = utils.load_vocab(vocab, 'source')
self.code_vocab = utils.load_vocab(vocab, 'code')
self.ast_vocab = utils.load_vocab(vocab, 'ast')
self.nl_vocab = utils.load_vocab(vocab, 'nl')
# vocabulary
self.source_vocab_size = len(self.source_vocab)
self.code_vocab_size = len(self.code_vocab)
self.ast_vocab_size = len(self.ast_vocab)
self.nl_vocab_size = len(self.nl_vocab)
logger.info('Size of source vocabulary: {} -> {}'.format(self.source_vocab.origin_size, self.source_vocab_size))
logger.info('Size of code vocabulary: {} -> {}'.format(self.code_vocab.origin_size, self.code_vocab_size))
logger.info('Size of ast vocabulary: {}'.format(self.ast_vocab_size))
logger.info('Size of nl vocabulary: {} -> {}'.format(self.nl_vocab.origin_size, self.nl_vocab_size))
logger.info('Vocabularies are successfully built')
# model
logger.info('-' * 100)
logger.info('Building model')
self.model = models.Model(source_vocab_size=self.source_vocab_size,
code_vocab_size=self.code_vocab_size,
ast_vocab_size=self.ast_vocab_size,
nl_vocab_size=self.nl_vocab_size,
is_eval=True,
model=model)
# model device
logger.info('Model device: {}'.format(next(self.model.parameters()).device))
# log model statistic
logger.info('Trainable parameters: {}'.format(utils.human_format(utils.count_params(self.model))))
def run(self):
# load data
args_dict = self._default_configs()
args = dotdict(args_dict)
batchedData, maxTimeSteps, totalN = self.load_data(args,
mode=mode,
type=level)
model = model_fn(args, maxTimeSteps)
# count the num of params
num_params = count_params(model, mode='trainable')
all_num_params = count_params(model, mode='all')
model.config['trainable params'] = num_params
model.config['all params'] = all_num_params
print(model.config)
#with tf.Session(graph=model.graph) as sess:
with tf.Session() as sess:
# restore from stored model
if keep == True:
ckpt = tf.train.get_checkpoint_state(savedir)
if ckpt and ckpt.model_checkpoint_path:
model.saver.restore(sess, ckpt.model_checkpoint_path)
print('Model restored from:' + savedir)
else:
print('Initializing')
sess.run(model.initial_op)
for epoch in range(num_epochs):
## training
start = time.time()
if mode == 'train':
print('Epoch', epoch + 1, '...')
batchErrors = np.zeros(len(batchedData))
batchRandIxs = np.random.permutation(len(batchedData))
for batch, batchOrigI in enumerate(batchRandIxs):
batchInputs, batchTargetSparse, batchSeqLengths = batchedData[
batchOrigI]
batchTargetIxs, batchTargetVals, batchTargetShape = batchTargetSparse
feedDict = {
model.inputX: batchInputs,
model.targetIxs: batchTargetIxs,
model.targetVals: batchTargetVals,
model.targetShape: batchTargetShape,
model.seqLengths: batchSeqLengths
}
if level == 'cha':
if mode == 'train':
_, l, pre, y, er = sess.run([
model.optimizer, model.loss, model.predictions,
model.targetY, model.errorRate
],
feed_dict=feedDict)
batchErrors[batch] = er
print(
'\n{} mode, total:{},batch:{}/{},epoch:{}/{},train loss={:.3f},mean train CER={:.3f}\n'
.format(level, totalN, batch + 1,
len(batchRandIxs), epoch + 1,
num_epochs, l, er / batch_size))
elif mode == 'test':
l, pre, y, er = sess.run([
model.loss, model.predictions, model.targetY,
model.errorRate
],
feed_dict=feedDict)
batchErrors[batch] = er
print(
'\n{} mode, total:{},batch:{}/{},test loss={:.3f},mean test CER={:.3f}\n'
.format(level, totalN, batch + 1,
len(batchRandIxs), l, er / batch_size))
elif level == 'phn':
if mode == 'train':
_, l, pre, y = sess.run([
model.optimizer, model.loss, model.predictions,
model.targetY
],
feed_dict=feedDict)
er = get_edit_distance([pre.values], [y.values],
True, level)
print(
'\n{} mode, total:{},batch:{}/{},epoch:{}/{},train loss={:.3f},mean train PER={:.3f}\n'
.format(level, totalN, batch + 1,
len(batchRandIxs), epoch + 1,
num_epochs, l, er))
batchErrors[batch] = er * len(batchSeqLengths)
elif mode == 'test':
l, pre, y = sess.run(
[model.loss, model.predictions, model.targetY],
feed_dict=feedDict)
er = get_edit_distance([pre.values], [y.values],
True, level)
print(
'\n{} mode, total:{},batch:{}/{},test loss={:.3f},mean test PER={:.3f}\n'
.format(level, totalN, batch + 1,
len(batchRandIxs), l, er))
batchErrors[batch] = er * len(batchSeqLengths)
# NOTE:
if er / batch_size == 1.0:
break
if batch % 30 == 0:
print('Truth:\n' + output_to_sequence(y, type=level))
print('Output:\n' +
output_to_sequence(pre, type=level))
if mode == 'train' and (
(epoch * len(batchRandIxs) + batch + 1) % 20 == 0 or
(epoch == num_epochs - 1
and batch == len(batchRandIxs) - 1)):
checkpoint_path = os.path.join(savedir, 'model.ckpt')
model.saver.save(sess,
checkpoint_path,
global_step=epoch)
print('Model has been saved in {}'.format(savedir))
end = time.time()
delta_time = end - start
print('Epoch ' + str(epoch + 1) + ' needs time:' +
str(delta_time) + ' s')
if mode == 'train':
if (epoch + 1) % 1 == 0:
checkpoint_path = os.path.join(savedir, 'model.ckpt')
model.saver.save(sess,
checkpoint_path,
global_step=epoch)
print('Model has been saved in {}'.format(savedir))
epochER = batchErrors.sum() / totalN
print('Epoch', epoch + 1, 'mean train error rate:',
epochER)
logging(model,
logfile,
epochER,
epoch,
delta_time,
mode='config')
logging(model,
logfile,
epochER,
epoch,
delta_time,
mode=mode)
if mode == 'test':
with open(os.path.join(resultdir, level + '_result.txt'),
'a') as result:
result.write(output_to_sequence(y, type=level) + '\n')
result.write(
output_to_sequence(pre, type=level) + '\n')
result.write('\n')
epochER = batchErrors.sum() / totalN
print(' test error rate:', epochER)
logging(model, logfile, epochER, mode=mode)
def main():
parser = argparse.ArgumentParser()
## Required parameters
parser.add_argument(
"--bert_model_or_config_file",
default=None,
type=str,
required=True,
help=(
"Path of configuration file (if starting from scratch) or directory"
" containing checkpoint (if resuming) or directory containig a"
" pretrained model and tokenizer (if re-training)."))
# Use for resuming from checkpoint
parser.add_argument("--resume",
action='store_true',
help="Resume from checkpoint")
# Required if not resuming
parser.add_argument(
"--dir_train_data",
type=str,
help=
"Path of a directory containing training files (names must all match <lang>.train)"
)
parser.add_argument(
"--path_vocab",
type=str,
help=
"Path of a 2-column TSV file containing the vocab of chars and their frequency."
)
parser.add_argument(
"--output_dir",
type=str,
help="The output directory where the model checkpoints will be written."
)
## Other parameters
parser.add_argument(
"--mlm_only",
action="store_true",
help=
("Use only masked language modeling, no sentence pair classification "
" (e.g. if you only have unk.train in your training directory)"))
parser.add_argument(
"--avgpool_for_spc",
action="store_true",
help=
("Use average pooling of all last hidden states, rather than just the last hidden state of CLS, to do SPC. "
"Note that in either case, the pooled vector passes through a square linear layer and a tanh before the classification layer."
))
parser.add_argument(
"--sampling_alpha",
type=float,
default=1.0,
help=
"Dampening factor for relative frequencies used to compute language sampling probabilities"
)
parser.add_argument(
"--weight_relevant",
type=float,
default=1.0,
help=
"Relative sampling frequency of relevant languages wrt irrelevant languages"
)
parser.add_argument("--train_batch_size",
default=32,
type=int,
help="Total batch size for training.")
parser.add_argument(
"--seq_len",
default=128,
type=int,
help=
"Length of input sequences. Shorter seqs are padded, longer ones are trucated"
)
parser.add_argument(
"--min_freq",
default=1,
type=int,
help=
"Minimum character frequency. Characters whose frequency is under this threshold will be mapped to <UNK>"
)
parser.add_argument("--learning_rate",
default=1e-4,
type=float,
help="The initial learning rate for AdamW optimizer.")
parser.add_argument("--equal_betas",
action='store_true',
help="Use beta1=beta2=0.9 for AdamW optimizer.")
parser.add_argument(
"--correct_bias",
action='store_true',
help=
"Correct bias in AdamW optimizer (correct_bias=False is meant to reproduce BERT behaviour exactly."
)
parser.add_argument(
"--max_train_steps",
default=1000000,
type=int,
help=
"Maximum number of training steps to perform. Note: # optimization steps = # train steps / # accumulation steps."
)
parser.add_argument(
"--num_train_steps_per_epoch",
default=1000,
type=int,
help=
"Number of training steps that equals one epoch. Note: # optimization steps = # train steps / # accumulation steps."
)
parser.add_argument(
"--num_warmup_steps",
default=10000,
type=int,
help=
"Number of optimization steps (i.e. training steps / accumulation steps) to perform linear learning rate warmup for. "
)
parser.add_argument(
'--grad_accum_steps',
type=int,
default=1,
help=
"Number of training steps (i.e. batches) to accumualte before performing a backward/update pass."
)
parser.add_argument(
"--num_gpus",
type=int,
default=-1,
help="Num GPUs to use for training (0 for none, -1 for all available)")
parser.add_argument("--local_rank",
type=int,
default=-1,
help="local_rank for distributed training on gpus")
parser.add_argument('--seed',
type=int,
default=42,
help="random seed for initialization")
args = parser.parse_args()
# These args are required if we are not resuming from checkpoint
if not args.resume:
assert args.dir_train_data is not None
assert args.path_vocab is not None
assert args.output_dir is not None
# Check whether we are starting from scratch, resuming from a checkpoint, or retraining a pretrained model
from_scratch = (not args.resume) and (not os.path.isdir(
args.bert_model_or_config_file))
retraining = (not args.resume) and (not from_scratch)
# Load config. Load or create checkpoint data.
if from_scratch:
logger.info("***** Starting pretraining job from scratch *******")
config = BertConfig.from_json_file(args.bert_model_or_config_file)
checkpoint_data = {}
elif retraining:
logger.info(
"***** Starting pretraining job from pre-trained model *******")
logger.info("Loading pretrained model...")
model = BertModelForMaskedLM.from_pretrained(
args.bert_model_or_config_file)
config = model.config
checkpoint_data = {}
elif args.resume:
logger.info("***** Resuming pretraining job *******")
logger.info("Loading checkpoint...")
checkpoint_path = os.path.join(args.bert_model_or_config_file,
"checkpoint.tar")
checkpoint_data = torch.load(checkpoint_path)
# Make sure we haven't already done the maximum number of optimization steps
if checkpoint_data["global_step"] >= checkpoint_data["max_opt_steps"]:
msg = "We have already done %d optimization steps." % checkpoint_data[
"global_step"]
raise RuntimeError(msg)
logger.info("Resuming from global step %d" %
checkpoint_data["global_step"])
# Replace args with initial args for this job, except for num_gpus, seed and model directory
current_num_gpus = args.num_gpus
current_seed = args.seed
checkpoint_dir = args.bert_model_or_config_file
args = deepcopy(checkpoint_data["initial_args"])
args.num_gpus = current_num_gpus
args.seed = current_seed
args.bert_model_or_config_file = checkpoint_dir
args.resume = True
logger.info("Args (most have been reloaded from checkpoint): %s" %
args)
# Load config
config_path = os.path.join(args.bert_model_or_config_file,
"config.json")
config = BertConfig.from_json_file(config_path)
# Check args
assert args.sampling_alpha >= 0 and args.sampling_alpha <= 1
assert args.weight_relevant > 0
if args.grad_accum_steps < 1:
raise ValueError(
"Invalid grad_accum_steps parameter: {}, should be >= 1".format(
args.grad_accum_steps))
train_paths = glob.glob(os.path.join(args.dir_train_data, "*.train"))
assert len(train_paths) > 0
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
if (not args.resume) and len(os.listdir(args.output_dir)) > 0:
msg = "Directory %s is not empty" % args.output_dir
raise ValueError(msg)
# Make or load tokenizer
if args.resume or retraining:
logger.info("Loading tokenizer...")
tokenizer_path = os.path.join(args.bert_model_or_config_file,
"tokenizer.pkl")
with open(tokenizer_path, "rb") as f:
tokenizer = pickle.load(f)
elif from_scratch:
logger.info("Making tokenizer...")
assert os.path.exists(args.path_vocab)
tokenizer = CharTokenizer(args.path_vocab)
if args.min_freq > 1:
tokenizer.trim_vocab(args.min_freq)
# Adapt vocab size in config
config.vocab_size = len(tokenizer.vocab)
# Save tokenizer
fn = os.path.join(args.output_dir, "tokenizer.pkl")
with open(fn, "wb") as f:
pickle.dump(tokenizer, f)
logger.info("Size of vocab: {}".format(len(tokenizer.vocab)))
# Copy config in output directory
if not args.resume:
config_path = os.path.join(args.output_dir, "config.json")
config.to_json_file(config_path)
# What GPUs do we use?
if args.num_gpus == -1:
args.device = torch.device(
"cuda" if torch.cuda.is_available() else "cpu")
args.n_gpu = torch.cuda.device_count()
device_ids = None
else:
args.device = torch.device("cuda" if torch.cuda.is_available()
and args.num_gpus > 0 else "cpu")
args.n_gpu = args.num_gpus
if args.n_gpu > 1:
device_ids = list(range(args.n_gpu))
if args.local_rank != -1:
torch.cuda.set_device(args.local_rank)
args.device = torch.device("cuda", args.local_rank)
args.n_gpu = 1
# Initializes the distributed backend which will take care of sychronizing nodes/GPUs
torch.distributed.init_process_group(backend='nccl')
logger.info("device: {} n_gpu: {}, distributed training: {}".format(
args.device, args.n_gpu, bool(args.local_rank != -1)))
# Seed RNGs
np.random.seed(args.seed)
torch.manual_seed(args.seed)
if args.n_gpu > 0:
torch.cuda.manual_seed_all(args.seed)
# Prepare model
if from_scratch or args.resume:
model = BertForMaskedLM(config)
if args.resume:
model.load_state_dict(checkpoint_data["model_state_dict"])
model.to(args.device)
# Prepare pooler (if we are doing SPC)
if args.mlm_only:
pooler = None
else:
pooler = Pooler(model.config.hidden_size,
cls_only=(not args.avgpool_for_spc))
if args.resume:
pooler.load_state_dict(checkpoint_data["pooler_state_dict"])
pooler.to(args.device)
# Distributed or parallel?
if args.local_rank != -1:
try:
from apex.parallel import DistributedDataParallel as DDP
except ImportError:
raise ImportError(
"Please install apex from https://www.github.com/nvidia/apex to use distributed training."
)
model = DDP(model)
if not args.mlm_only:
pooler = DDP(pooler)
elif args.n_gpu > 1:
model = torch.nn.DataParallel(model, device_ids=device_ids)
pooler = torch.nn.DataParallel(pooler, device_ids=device_ids)
# Log some info on the model
logger.info("Model config: %s" % repr(model.config))
logger.info("Nb params: %d" % count_params(model))
if not args.mlm_only:
logger.info("Nb params in pooler: %d" % count_params(pooler))
# Check if there is unk training data.
path_unk = check_for_unk_train_data(train_paths)
# Get training data
max_seq_length = args.seq_len + 2 # We add 2 for CLS and SEP
logger.info("Preparing dataset using data from %s" % args.dir_train_data)
if args.mlm_only:
# We only want to do MLM
train_dataset_spc = None
train_dataset_mlm = BertDatasetForMLM(
train_paths,
tokenizer,
max_seq_length,
sampling_alpha=args.sampling_alpha,
weight_relevant=args.weight_relevant,
encoding="utf-8",
seed=args.seed)
else:
# We want do to SLC and MLM. If unk data is present, we remove
# it from the paths provided to BertLabeledDataset.
if path_unk is not None:
train_paths.remove(path_unk)
train_dataset_spc = BertDatasetForSPCAndMLM(
train_paths,
tokenizer,
max_seq_length,
sampling_alpha=args.sampling_alpha,
weight_relevant=args.weight_relevant,
encoding="utf-8",
seed=args.seed)
if path_unk is None:
train_dataset_mlm = None
else:
# In this case we use a BertDatasetForMLM for the unk
# data. Both datasets will be of the same size. The latter
# is used for MLM only.
train_dataset_mlm = BertDatasetForMLM(
[path_unk],
tokenizer,
max_seq_length,
sampling_alpha=args.sampling_alpha,
weight_relevant=args.weight_relevant,
encoding="utf-8",
seed=args.seed)
assert len(train_dataset_spc) == len(train_dataset_mlm)
# Check length of dataset
dataset_length = len(
train_dataset_spc) if train_dataset_spc is not None else len(
train_dataset_mlm)
# Store optimization steps performed and maximum number of optimization steps
if not args.resume:
checkpoint_data["global_step"] = 0
checkpoint_data[
"max_opt_steps"] = args.max_train_steps // args.grad_accum_steps
# Compute number of optimization steps per epoch
num_opt_steps_per_epoch = args.num_train_steps_per_epoch // args.grad_accum_steps
# Compute number of epochs necessary to reach the maximum number of optimization steps
opt_steps_left = checkpoint_data["max_opt_steps"] - checkpoint_data[
"global_step"]
args.num_epochs = math.ceil(opt_steps_left / num_opt_steps_per_epoch)
# Log some info before training
logger.info("*** Training info: ***")
logger.info("Max training steps: %d" % args.max_train_steps)
logger.info("Gradient accumulation steps: %d" % args.grad_accum_steps)
logger.info("Max optimization steps: %d" %
checkpoint_data["max_opt_steps"])
if args.resume:
logger.info("Nb optimization steps done so far: %d" %
checkpoint_data["global_step"])
logger.info("Total dataset size: %d examples" % (dataset_length))
logger.info("Batch size: %d" % args.train_batch_size)
logger.info("# training steps/epoch: %d" %
(args.num_train_steps_per_epoch))
logger.info("# optimization steps/epoch: %d" % (num_opt_steps_per_epoch))
logger.info("# epochs to do: %d" % (args.num_epochs))
# Prepare optimizer
logger.info("Preparing optimizer...")
np_list = list(model.named_parameters())
if not args.mlm_only:
np_list += list(pooler.named_parameters())
no_decay = ['bias', 'LayerNorm.bias', 'LayerNorm.weight']
opt_params = [{
'params':
[p for n, p in np_list if not any(nd in n for nd in no_decay)],
'weight_decay':
0.01
}, {
'params': [p for n, p in np_list if any(nd in n for nd in no_decay)],
'weight_decay':
0.0
}]
if args.equal_betas:
betas = (0.9, 0.9)
else:
betas = (0.9, 0.999)
optimizer = AdamW(
opt_params,
lr=args.learning_rate,
betas=betas,
correct_bias=args.correct_bias
) # To reproduce BertAdam specific behaviour, use correct_bias=False
if args.resume:
optimizer.load_state_dict(checkpoint_data["optimizer_state_dict"])
# Prepare scheduler
logger.info("Preparing learning rate scheduler...")
scheduler = get_linear_schedule_with_warmup(
optimizer,
num_warmup_steps=args.num_warmup_steps,
num_training_steps=checkpoint_data["max_opt_steps"])
if args.resume:
scheduler.load_state_dict(checkpoint_data["scheduler_state_dict"])
logger.info("Current learning rate: %f" % scheduler.get_last_lr()[0])
# Save initial training args
if not args.resume:
checkpoint_data["initial_args"] = args
# Prepare training log
time_str = datetime.now().strftime("%Y%m%d%H%M%S")
train_log_path = os.path.join(args.output_dir, "%s.train.log" % time_str)
args.train_log_path = train_log_path
# Train
if args.mlm_only:
train(model,
None,
tokenizer,
optimizer,
scheduler,
train_dataset_mlm,
args,
checkpoint_data,
extra_mlm_dataset=None)
else:
train(model,
pooler,
tokenizer,
optimizer,
scheduler,
train_dataset_spc,
args,
checkpoint_data,
extra_mlm_dataset=train_dataset_mlm)
run_tstart = time.time()
for epoch in range(args.epochs):
train(model, optimizer, epoch)
run_time = time.time() - run_tstart
run_loss, run_acc = test(model, optimizer)
if args.runs > 1:
print("Run #{run} Test -- time: {time}s acc: {acc:.2f}%".format(
run=run, time=run_time, acc=100 * run_acc),
flush=True)
except KeyboardInterrupt:
args.runs = run
break
total_loss += run_loss
total_acc += run_acc
total_time += run_time
total_loss, total_acc, total_time = map(lambda x: x / args.runs,
[total_loss, total_acc, total_time])
print("Optimization on dataset \"{dataset}\" Finished!".format(
dataset=args.dataset))
print("#Parameters: {param_count}".format(param_count=count_params(model)))
print("Average time elapsed: {:.4f}s".format(total_time))
# Testing
print("Test set results:", "avg loss= {:.4f}".format(total_loss),
"avg accuracy= {:.4f}".format(total_acc))
def train():
tf.global_variables_initializer().run()
could_load, checkpoint_counter = load()
if could_load:
start_epoch = (int)(checkpoint_counter / num_batches)
start_batch_id = checkpoint_counter - start_epoch * num_batches
counter = checkpoint_counter
print("Checkpoint Load Successed")
else:
start_epoch = 0
start_batch_id = 0
counter = 1
print("train from scratch...")
train_iter=[]
train_loss=[]
utils.count_params()
print("Total image:{}".format(len(train_img)))
print("Total epoch:{}".format(args.num_epochs))
print("Batch size:{}".format(args.batch_size))
print("Learning rate:{}".format(args.learning_rate))
print("Checkpoint step:{}".format(args.checkpoint_step))
print("Data Argument:")
print("h_flip: {}".format(args.h_flip))
print("v_flip: {}".format(args.v_flip))
print("rotate: {}".format(args.rotation))
print("clip size: {}".format(args.clip_size))
for i in range(start_epoch,args.num_epochs):
id_list = np.random.permutation(len(train_img))
epoch_time=time.time()
for j in range(start_batch_id,num_batches):
img_d=[]
lab_d=[]
for ind in range(args.batch_size):
id = id_list[j * args.batch_size + ind]
img_d.append(train_img[id])
lab_d.append(train_label[id])
x_batch, y_batch = load_batch(img_d,lab_d,args)
feed_dict = {img: x_batch,
label: y_batch
}
loss_tmp = []
_, loss, pred1 = sess.run([train_step, sigmoid_cross_entropy_loss, pred], feed_dict=feed_dict)
loss_tmp.append(loss)
if (counter % 100 == 0):
tmp = np.mean(loss_tmp)
train_iter.append(counter)
train_loss.append(tmp)
print('Epoch', i, '|Iter', counter, '|Loss', tmp)
counter += 1
start_batch_id=0
print('Time:', time.time() - epoch_time)
#if((i+1)%10==0 ):#lr dst from 10 every 10 epoches by 0.1
#learning_rate = 0.1 * learning_rate
#last_checkpoint_name = "checkpoint/latest_model_epoch_" + "_pspet.ckpt"
# print("Saving latest checkpoint")
# saver.save(sess, last_checkpoint_name)
if((i+1)%args.checkpoint_step==0):#save 20,30,40,50 checkpoint
args.learning_rate=0.1*args.learning_rate
print(args.learning_rate)
saver.save(sess,'./checkpoint/model.ckpt',global_step=counter,write_meta_graph=True)
"""
host = host_subplot(111)
plt.subplots_adjust(right=0.8)
p1, = host.plot(train_iter, train_loss, label="training loss")
host.legend(loc=5)
host.axis["left"].label.set_color(p1.get_color())
host.set_xlim([0, counter])
plt.draw()
plt.show()
"""
fig1, ax1 = plt.subplots(figsize=(11, 8))
ax1.plot(train_iter, train_loss)
ax1.set_title("Training loss vs Iter")
ax1.set_xlabel("Iter")
ax1.set_ylabel("Training loss")
plt.savefig('Training loss_vs_Iter.png')
plt.clf()
remain_time=(args.num_epochs - 1 - i) * (time.time() - epoch_time)
m, s = divmod(remain_time, 60)
h, m = divmod(m, 60)
print("Remaining training time = %d hours %d minutes %d seconds\n" % (h, m, s))
def num_params(self):
return count_params(self)
def main():
args = parse_args()
if args.name is None:
if args.deepsupervision:
args.name = '%s_%s_wDS' % (args.dataset, args.arch)
else:
args.name = '%s_%s_woDS' % (args.dataset, args.arch)
if not os.path.exists('models/%s' % args.name):
os.makedirs('models/%s' % args.name)
print('Config -----')
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)))
print('------------')
with open('models/%s/args.txt' % args.name, 'w') as f:
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)), file=f)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
# define loss function (criterion)
if args.loss == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[args.loss]().cuda()
cudnn.benchmark = True
DATA_PATH = '../../Datasets/'
img_paths = []
mask_paths = []
for class_folder in os.listdir(DATA_PATH):
FOLDER_PATH = os.path.join(DATA_PATH, class_folder)
for patient_folder in os.listdir(FOLDER_PATH):
patient_folder = os.path.join(FOLDER_PATH, patient_folder)
if os.path.isdir(patient_folder):
if (os.path.isfile(
os.path.join(patient_folder, 'AP/Ap_Pedicle.png'))):
mask_paths.append(
os.path.join(patient_folder, 'AP/Ap_Pedicle.png'))
img_paths.append(os.path.join(patient_folder, "AP.jpg"))
c = list(zip(img_paths, mask_paths))
random.shuffle(c)
img_paths, mask_paths = zip(*c)
img_paths = np.array(img_paths)
mask_paths = np.array(mask_paths)
train_img_paths, val_img_paths, train_mask_paths, val_mask_paths = \
train_test_split(img_paths, mask_paths, test_size=0.05, random_state=41)
# create model
print("=> creating model %s" % args.arch)
model = archs.__dict__[args.arch](args)
model = model.cuda()
print(count_params(model))
if args.optimizer == 'Adam':
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
elif args.optimizer == 'SGD':
optimizer = optim.SGD(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay,
nesterov=args.nesterov)
train_dataset = Dataset(args, train_img_paths, train_mask_paths, args.aug)
val_dataset = Dataset(args, val_img_paths, val_mask_paths)
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
log = pd.DataFrame(
index=[],
columns=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
best_iou = 0
trigger = 0
for epoch in range(args.epochs):
print('Epoch [%d/%d]' % (epoch, args.epochs))
# train for one epoch
train_log = train(args, train_loader, model, criterion, optimizer,
epoch)
# evaluate on validation set
val_log = validate(args, val_loader, model, criterion)
print('loss %.4f - iou %.4f - val_loss %.4f - val_iou %.4f' %
(train_log['loss'], train_log['iou'], val_log['loss'],
val_log['iou']))
tmp = pd.Series(
[
epoch,
args.lr,
train_log['loss'],
train_log['iou'],
val_log['loss'],
val_log['iou'],
],
index=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
log = log.append(tmp, ignore_index=True)
log.to_csv('models/%s/log.csv' % args.name, index=False)
trigger += 1
if val_log['iou'] > best_iou:
torch.save(model.state_dict(), './models/%s/model.pth' % args.name)
best_iou = val_log['iou']
print("=> saved best model")
trigger = 0
# early stopping
if not args.early_stop is None:
if trigger >= args.early_stop:
print("=> early stopping")
break
torch.cuda.empty_cache()
import data
from deepsense import neptune
ctx = neptune.Context()
model_name = ctx.params['model']
epochs = ctx.params['epochs']
learning_rate = ctx.params['learning_rate']
ctx.tags.append(model_name)
# data
dataloaders = data.get_dataloaders('/input', batch_size=128)
# network
model = models.MODELS[model_name]
optimizer = optim.Adam(model.parameters(), lr=learning_rate)
criterion = nn.CrossEntropyLoss(size_average=False)
print("Network created. Number of parameters:")
print(utils.count_params(model))
# training
trained_model = utils.train_model(model,
criterion,
optimizer,
dataloaders,
num_epochs=epochs)
utils.save_all(trained_model)
def _spec(net, xentPerExample, is_accum=False, nohess=False, randvec=False):
"""returns principal eig of the hessian"""
if nohess:
net.valtotEager = net.bzEager = net.valEager = net.valtotAccum = net.bzAccum = net.valAccum = tf.constant(0, tf.float32)
net.projvec = net.projvec_op = net.projvec_corr = tf.constant(0, tf.float32)
return
batchsize = tf.shape(xentPerExample)[0]
xent = tf.reduce_sum(xentPerExample)
# decide weights from which to compute the spectral radius
print('Number of trainable weights: ' + str(utils.count_params(tf.trainable_variables())))
if not net.args.specreg_bn: # don't include batch norm weights
net.regularizable = []
for var in tf.trainable_variables():
if var.op.name.find('logit/dense/kernel') > -1 or var.op.name.find(r'DW') > -1:
net.regularizable.append(var)
print('Number of regularizable weights: ' + str(utils.count_params(net.regularizable)))
else:
net.regularizable = tf.trainable_variables() # do include bn weights
print('Still zeroing out bias and bn variables in hessian calculation in utils.filtnorm function')
# create initial projection vector (randomly and normalized)
projvec_init = [np.random.randn(*r.get_shape().as_list()) for r in net.regularizable]
magnitude = np.sqrt(np.sum([np.sum(p**2) for p in projvec_init]))
projvec_init = [p/magnitude for p in projvec_init]
# projection vector tensor variable
net.count = net.count + 1 if hasattr(net, 'count') else 0
with tf.variable_scope('projvec/'+str(net.count)):
net.projvec = [tf.get_variable(name=r.op.name, dtype=tf.float32, shape=r.get_shape(),
trainable=False, initializer=tf.constant_initializer(p))
for r,p in zip(net.regularizable, projvec_init)]
# compute filter normalization
print('normalization scheme: '+net.args.normalizer)
if net.args.normalizer == None or net.args.normalizer=='None':
projvec_mul_normvalues = net.projvec
else:
if net.args.normalizer == 'filtnorm': normalizer = utils.filtnorm
elif net.args.normalizer == 'layernorm': normalizer = utils.layernorm
elif net.args.normalizer == 'layernormdev': normalizer = utils.layernormdev
net.normvalues = normalizer(net.regularizable)
projvec_mul_normvalues = [n*p for n,p in zip(net.normvalues, net.projvec)]
# get gradient of loss wrt inputs
tstart = time.time(); gradLoss = tf.gradients(xent, net.regularizable); print('Built gradLoss: ' + str(time.time() - tstart) + ' s')
# get hessian vector product
tstart = time.time()
hessVecProd = tf.gradients(gradLoss, net.regularizable, projvec_mul_normvalues)
# hessVecProd = [h*n for h,n in zip(hessVecProd, net.normvalues)]
print('Built hessVecProd: ' + str(time.time() - tstart) + ' s')
# build graph for full-batch hessian calculations which require accum ops and storage variables (for validation)
if is_accum:
# create op to accumulate gradients
with tf.variable_scope('accum'):
hessvecprodAccum = [tf.Variable(tf.zeros_like(h), trainable=False, name=h.op.name) for h in hessVecProd]
batchsizeAccum = tf.Variable(0, trainable=False, name='batchsizeAccum')
net.zero_op = [a.assign(tf.zeros_like(a)) for a in hessvecprodAccum] + [batchsizeAccum.assign(0)]
net.accum_op = [a.assign_add(g) for a,g in zip(hessvecprodAccum, hessVecProd)] + [batchsizeAccum.assign_add(batchsize)]
# compute the projected projection vector using accumulated hvps
nextProjvec = compute_nextProjvec(net.projvec, hessvecprodAccum, net.projvec_beta, randvec=randvec)
print('nextProjvec using accumed hvp')
# hooks for total eigenvalue, batch size, and eigenvalue
net.valtotAccum = utils.list2dotprod(net.projvec, hessvecprodAccum)
net.bzAccum = tf.to_float(batchsizeAccum)
net.valAccum = net.valtotAccum / net.bzAccum
# build graph for on-the-fly per-batch hessian calcuations (for training)
else:
# compute the projected projection vector using instantaneous hvp
nextProjvec = compute_nextProjvec(net.projvec, hessVecProd, net.projvec_beta, randvec=randvec)
print('nextProjvec using instant hvp and randvec is', randvec)
# hooks for total eigenvalue, batch size, and eigenvalue
net.valtotEager = utils.list2dotprod(net.projvec, hessVecProd)
net.bzEager = tf.to_float(batchsize)
net.valEager = net.valtotEager / net.bzEager
# dotprod and euclidean distance of new projection vector from previous
net.projvec_corr = utils.list2dotprod(nextProjvec, net.projvec)
# op to assign the new projection vector for next iteration
with tf.control_dependencies([net.projvec_corr]):
with tf.variable_scope('projvec_op'):
net.projvec_op = [tf.assign(p,n) for p,n in zip(net.projvec, nextProjvec)]
def train(self,args):
''' import data, train model, save model
'''
args.data_dir = args.data_dir+args.style+'/'
args.save_dir = args.save_dir+args.style+'/'
print(args)
if args.attention is True:
print('attention mode')
text_parser = TextParser(args)
args.vocab_size = text_parser.vocab_size
if args.pretrained is True:
raise ValueError('pretrained has bug now, so don"t set it to be True now!!!')
if args.keep is False:
raise ValueError('when pre-trained is True, keep must be true!')
print("pretrained and keep mode...")
print("restoring pretrained model file")
ckpt = tf.train.get_checkpoint_state("/home/pony/github/jaylyrics_generation_tensorflow/data/pre-trained/")
if os.path.exists(os.path.join("./data/pre-trained/",'config.pkl')) and \
os.path.exists(os.path.join("./data/pre-trained/",'words_vocab.pkl')) and \
ckpt and ckpt.model_checkpoint_path:
with open(os.path.join("./data/pre-trained/", 'config.pkl'), 'rb') as f:
saved_model_args = cPickle.load(f)
with open(os.path.join("./data/pre-trained/", 'words_vocab.pkl'), 'rb') as f:
saved_words, saved_vocab = cPickle.load(f)
else:
raise ValueError('configuration doesn"t exist!')
else:
ckpt = tf.train.get_checkpoint_state(args.save_dir)
if args.keep is True and args.pretrained is False:
# check if all necessary files exist
if os.path.exists(os.path.join(args.save_dir,'config.pkl')) and \
os.path.exists(os.path.join(args.save_dir,'words_vocab.pkl')) and \
ckpt and ckpt.model_checkpoint_path:
with open(os.path.join(args.save_dir, 'config.pkl'), 'rb') as f:
saved_model_args = cPickle.load(f)
with open(os.path.join(args.save_dir, 'words_vocab.pkl'), 'rb') as f:
saved_words, saved_vocab = cPickle.load(f)
else:
raise ValueError('configuration doesn"t exist!')
if args.model == 'seq2seq_rnn':
model = Model_rnn(args)
else:
# TO ADD OTHER MODEL
pass
trainable_num_params = count_params(model,mode='trainable')
all_num_params = count_params(model,mode='all')
args.num_trainable_params = trainable_num_params
args.num_all_params = all_num_params
with open(os.path.join(args.save_dir, 'config.pkl'), 'wb') as f:
cPickle.dump(args, f)
with open(os.path.join(args.save_dir, 'words_vocab.pkl'), 'wb') as f:
cPickle.dump((text_parser.vocab_dict, text_parser.vocab_list), f)
with tf.Session() as sess:
if args.keep is True:
print('Restoring')
model.saver.restore(sess, ckpt.model_checkpoint_path)
else:
print('Initializing')
sess.run(model.initial_op)
sess.run(tf.assign(model.lr, args.learning_rate))
for e in range(args.num_epochs):
start = time.time()
model.initial_state = tf.convert_to_tensor(model.initial_state)
state = model.initial_state.eval()
total_loss = []
for b in range(text_parser.num_batches):
x, y = text_parser.next_batch()
if args.attention is True:
attention_states = sess.run(tf.truncated_normal([args.batch_size,
model.attn_length, model.attn_size],
stddev=0.1,dtype=tf.float32))
feed = {model.input_data: x, model.targets: y,
model.initial_state: state,
model.attention_states:attention_states}
else:
feed = {model.input_data: x,
model.targets: y,
model.initial_state: state}
train_loss, state, _ = sess.run([model.cost,
model.final_state,
model.train_op],
feed)
total_loss.append(train_loss)
print("{}/{} (epoch {}), train_loss = {:.3f}" \
.format(e * text_parser.num_batches + b, \
args.num_epochs * text_parser.num_batches, \
e, train_loss))
if (e*text_parser.num_batches+b)%args.save_every==0:
checkpoint_path = os.path.join(args.save_dir, 'model.ckpt')
model.saver.save(sess, checkpoint_path, global_step = e)
print("model has been saved in:"+str(checkpoint_path))
end = time.time()
delta_time = end - start
ave_loss = np.array(total_loss).mean()
logging(model,ave_loss,e,delta_time,mode='train')
if ave_loss < 0.1:
checkpoint_path = os.path.join(args.save_dir, 'model.ckpt')
model.saver.save(sess, checkpoint_path, global_step = e)
print("model has been saved in:"+str(checkpoint_path))
break
losses = unweighted_loss * class_weights
else:
if args.loss_func == "cross_entropy":
losses = tf.nn.softmax_cross_entropy_with_logits(logits=network,
labels=net_output)
elif args.loss_func == "lovasz":
losses = utils.lovasz_softmax(probas=network, labels=net_output)
loss = tf.reduce_mean(losses)
opt = tf.train.AdamOptimizer(0.0001).minimize(
loss, var_list=[var for var in tf.trainable_variables()])
saver = tf.train.Saver(max_to_keep=1000)
sess.run(tf.global_variables_initializer())
utils.count_params()
# If a pre-trained ResNet is required, load the weights.
# This must be done AFTER the variables are initialized with sess.run(tf.global_variables_initializer())
if init_fn is not None:
init_fn(sess)
# Load a previous checkpoint if desired
model_checkpoint_name = "checkpoints/latest_model_" + args.model + "_" + args.dataset + ".ckpt"
if args.continue_training or not args.mode == "train":
print('Loaded latest model checkpoint')
saver.restore(sess, model_checkpoint_name)
avg_scores_per_epoch = []
# Load the data
tf.summary.scalar("lambda", decayed_reg)
summary_op = tf.summary.merge_all()
name = str(lr) + '_' + str(bs) + '_' + str(nn)
train_writer = tf.summary.FileWriter(tensorboard_log + name + '/train/', graph = sess.graph)
val_writer = tf.summary.FileWriter(tensorboard_log + name + '/val/')
# Initialize all variables
sess.run(tf.global_variables_initializer())
# Load the pretrained weights into the non-trainable layer
model_rgb.load_params(sess, params_dir_rgb, trainable=False)
model_depth.load_params(sess, params_dir_depth, trainable=False)
print("\nHyper-parameters: lr={}, #neurons={}, bs={}, l2={}, max_norm={}, dropout_rate={}".format(lr,nn,bs,aa,mn,do))
print("Number of trainable parameters = {}".format(count_params(trainable_variables_rnn)+count_params(trainable_variables_conv1x1)))
print("\n{} Generate features from training set".format(datetime.now()))
tb_train_count=0
tb_val_count = 0
# Loop over number of epochs
num_samples = 0
# Training set
sess.run(training_init_op)
# Progress bar setting
bar = progressbar.ProgressBar(maxval=tr_batches_per_epoch, widgets=[progressbar.Bar('=', '[', ']'), ' ', progressbar.Percentage()])
def test_count_params(self):
linear = nn.Linear(123, 42)
n_weights = 123 * 42
n_bias = 42
n_total = n_weights + n_bias
self.assertEqual(n_total, count_params(linear))
def main():
args = parse_args()
if args.name is None:
if args.deepsupervision:
args.name = '%s_%s_wDS' % (args.dataset, args.arch)
else:
args.name = '%s_%s_woDS' % (args.dataset, args.arch)
if not os.path.exists('models/%s' % args.name):
os.makedirs('models/%s' % args.name)
print('Config -----')
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)))
print('------------')
with open('models/%s/args.txt' % args.name, 'w') as f:
for arg in vars(args):
print('%s: %s' % (arg, getattr(args, arg)), file=f)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
# define loss function (criterion)
if args.loss == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[args.loss]().cuda()
cudnn.benchmark = True
DATA_PATH = '../../Datasets/'
img_paths = []
mask_paths = []
for class_folder in os.listdir(DATA_PATH):
FOLDER_PATH = os.path.join(DATA_PATH, class_folder)
for patient_folder in os.listdir(FOLDER_PATH):
patient_folder = os.path.join(FOLDER_PATH, patient_folder)
if os.path.isdir(patient_folder):
if (os.path.isfile(
os.path.join(patient_folder, 'LAT/Lat_Vertebra.png'))):
mask_paths.append(
os.path.join(patient_folder, 'LAT/Lat_Vertebra.png'))
img_paths.append(os.path.join(patient_folder, "LAT.jpg"))
c = list(zip(img_paths, mask_paths))
random.shuffle(c)
img_paths, mask_paths = zip(*c)
img_paths = np.array(img_paths)
mask_paths = np.array(mask_paths)
k = 10
kf = KFold(n_splits=k)
fold_num = 0
mean_ious = []
for train_index, test_index in kf.split(img_paths):
train_img_paths, val_img_paths, train_mask_paths, val_mask_paths = \
train_test_split(img_paths[train_index], mask_paths[train_index], test_size=0.08, random_state=41)
# create model
print("=> creating model %s for fold %s" % (args.arch, fold_num))
fold_num += 1
model = archs.__dict__[args.arch](args)
model = model.cuda()
print(count_params(model))
if args.optimizer == 'Adam':
optimizer = optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
elif args.optimizer == 'SGD':
optimizer = optim.SGD(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay,
nesterov=args.nesterov)
train_dataset = Dataset(args, train_img_paths, train_mask_paths,
args.aug)
val_dataset = Dataset(args, val_img_paths, val_mask_paths)
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
log = pd.DataFrame(
index=[],
columns=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
best_iou = 0
trigger = 0
for epoch in range(args.epochs):
print('Epoch [%d/%d]' % (epoch, args.epochs))
# train for one epoch
train_log = train(args, train_loader, model, criterion, optimizer,
epoch)
# evaluate on validation set
val_log = validate(args, val_loader, model, criterion)
print('loss %.4f - iou %.4f - val_loss %.4f - val_iou %.4f' %
(train_log['loss'], train_log['iou'], val_log['loss'],
val_log['iou']))
tmp = pd.Series(
[
epoch,
args.lr,
train_log['loss'],
train_log['iou'],
val_log['loss'],
val_log['iou'],
],
index=['epoch', 'lr', 'loss', 'iou', 'val_loss', 'val_iou'])
log = log.append(tmp, ignore_index=True)
log.to_csv('models/%s/log.csv' % args.name, index=False)
trigger += 1
if val_log['iou'] > best_iou:
torch.save(model.state_dict(),
'./models/%s/model.pth' % args.name)
best_iou = val_log['iou']
print("=> saved best model")
trigger = 0
# early stopping
if not args.early_stop is None:
if trigger >= args.early_stop:
print("=> early stopping")
break
torch.cuda.empty_cache()
args = joblib.load('models/%s/args.pkl' % args.name)
if not os.path.exists('output/%s' % args.name):
os.makedirs('output/%s' % args.name)
joblib.dump(args, 'models/%s/args.pkl' % args.name)
# create model
print("=> Testing model %s" % args.arch)
model = archs.__dict__[args.arch](args)
model = model.cuda()
test_img_paths, test_mask_paths = img_paths[test_index], mask_paths[
test_index]
input_paths = test_img_paths
model.load_state_dict(torch.load('models/%s/model.pth' % args.name))
model.eval()
test_dataset = Dataset(args, test_img_paths, test_mask_paths)
test_loader = torch.utils.data.DataLoader(test_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
drop_last=False)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
with torch.no_grad():
for i, (input, target) in tqdm(enumerate(test_loader),
total=len(test_loader)):
input = input.cuda()
target = target.cuda()
# compute output
if args.deepsupervision:
output = model(input)[-1]
else:
output = model(input)
output = torch.sigmoid(output).data.cpu().numpy()
test_img_paths = test_img_paths[args.batch_size *
i:args.batch_size *
(i + 1)]
imsave(
os.path.join("./output/%s" % args.name,
str(i) + ".png"),
(output[0, 0, :, :] * 255).astype('uint8'))
torch.cuda.empty_cache()
# IoU
ious = []
for i in tqdm(range(len(test_mask_paths))):
input_img = cv2.imread(input_paths[i], 1)[:, :, 0]
input_img = cv2.resize(input_img, (256, 256))
mask = np.zeros((256, 256))
_mask = cv2.imread(test_mask_paths[i])[:, :, 0]
_mask = cv2.resize(_mask, (256, 256))
mask = np.maximum(mask, _mask)
pb = imread('output/%s/' % args.name + str(i) + ".png")
mask = mask.astype('float32') / 255
pb = pb.astype('float32') / 255
iou = iou_score(pb, mask)
ious.append(iou)
mean_ious.append(np.mean(ious))
print("\n")
print(mean_ious)
print(np.mean(mean_ious))
