def collect_eval_dir(root_uri):
eval_json_uris = list_paths(join(root_uri, 'eval'), ext='eval.json')
for eval_json_uri in eval_json_uris:
eval_json = file_to_json(eval_json_uri)
print(basename(dirname(eval_json_uri)))
print(eval_json['overall'][-1]['f1'])
print()
def collect_experiment(key, root_uri, output_dir, get_pred_package=False):
print('\nCollecting experiment {}...\n'.format(key))
if root_uri.startswith('s3://'):
predict_package_uris = list_paths(join(root_uri, key, 'bundle'), ext='predict_package.zip')
eval_json_uris = list_paths(join(root_uri, key, 'eval'), ext='eval.json')
else:
predict_package_uris = glob.glob(join(root_uri, key, 'bundle', '*', 'predict_package.zip'))
eval_json_uris = glob.glob(join(root_uri, key, 'eval', '*', 'eval.json'))
if len(predict_package_uris) > 1 or len(eval_json_uris) > 1:
print('Cannot collect from key with multiple experiments!!!')
return
if len(predict_package_uris) == 0 or len(eval_json_uris) == 0:
print('Missing output!!!')
return
predict_package_uri = predict_package_uris[0]
eval_json_uri = eval_json_uris[0]
make_dir(join(output_dir, key))
if get_pred_package:
download_or_copy(predict_package_uri, join(output_dir, key))
download_or_copy(eval_json_uri, join(output_dir, key))
eval_json = file_to_json(join(output_dir, key, 'eval.json'))
pprint.pprint(eval_json['overall'], indent=4)
def __init__(self, img_dir, annotation_uris, transforms=None):
self.img_dir = img_dir
self.annotation_uris = annotation_uris
self.transforms = transforms
self.imgs = []
self.img2id = {}
self.id2img = {}
self.id2boxes = defaultdict(lambda: [])
self.id2labels = defaultdict(lambda: [])
self.label2name = {}
for annotation_uri in annotation_uris:
ann_json = file_to_json(annotation_uri)
for img in ann_json['images']:
self.imgs.append(img['file_name'])
self.img2id[img['file_name']] = img['id']
self.id2img[img['id']] = img['file_name']
for ann in ann_json['annotations']:
img_id = ann['image_id']
box = ann['bbox']
label = ann['category_id']
box = torch.tensor(
[[box[1], box[0], box[1] + box[3], box[0] + box[2]]])
self.id2boxes[img_id].append(box)
self.id2labels[img_id].append(label)
self.id2boxes = dict([(id, torch.cat(boxes).float())
for id, boxes in self.id2boxes.items()])
self.id2labels = dict([(id, torch.tensor(labels))
for id, labels in self.id2labels.items()])
def get_label_names(coco_path):
categories = file_to_json(coco_path)['categories']
label2name = dict([(cat['id'], cat['name']) for cat in categories])
labels = ['background'
] + [label2name[i] for i in range(1,
len(label2name) + 1)]
return labels
def from_model_bundle(model_bundle_uri, tmp_dir):
model_bundle_path = download_if_needed(model_bundle_uri, tmp_dir)
model_bundle_dir = join(tmp_dir, 'model-bundle')
unzip(model_bundle_path, model_bundle_dir)
config_path = join(model_bundle_dir, 'config.json')
model_path = join(model_bundle_dir, 'model.pth')
cfg = build_config(file_to_json(config_path))
return cfg.get_learner()(cfg, tmp_dir, model_path=model_path)
def _run_command(cfg_json_uri, command, split_ind, num_splits):
tmp_root_dir = '/opt/data/tmp'
make_dir(tmp_root_dir)
tmp_dir_obj = tempfile.TemporaryDirectory(dir=tmp_root_dir)
tmp_dir = tmp_dir_obj.name
pipeline_cfg_dict = file_to_json(cfg_json_uri)
cfg = build_config(pipeline_cfg_dict)
pipeline = cfg.get_pipeline()(cfg, tmp_dir)
# TODO generalize this to work outside batch
if split_ind is None:
split_ind = int(os.environ.get('AWS_BATCH_JOB_ARRAY_INDEX', 0))
command_fn = getattr(pipeline, command)
if num_splits > 1:
print('Running {} command split {}/{}...'.format(
command, split_ind + 1, num_splits))
command_fn(split_ind=split_ind, num_splits=num_splits)
else:
print('Running {} command...'.format(command))
command_fn()
def train(self, tmp_dir):
"""Train a model.
This downloads any previous output saved to the train_uri,
starts training (or resumes from a checkpoint), periodically
syncs contents of train_dir to train_uri and after training finishes.
Args:
tmp_dir: (str) path to temp directory
"""
self.log_options()
# Sync output of previous training run from cloud.
train_uri = self.backend_opts.train_uri
train_dir = get_local_path(train_uri, tmp_dir)
make_dir(train_dir)
sync_from_dir(train_uri, train_dir)
# Get zip file for each group, and unzip them into chip_dir.
chip_dir = join(tmp_dir, 'chips')
make_dir(chip_dir)
for zip_uri in list_paths(self.backend_opts.chip_uri, 'zip'):
zip_path = download_if_needed(zip_uri, tmp_dir)
with zipfile.ZipFile(zip_path, 'r') as zipf:
zipf.extractall(chip_dir)
# Setup data loader.
batch_size = self.train_opts.batch_size
chip_size = self.task_config.chip_size
class_names = self.class_map.get_class_names()
databunch = build_databunch(chip_dir, chip_size, batch_size,
class_names)
log.info(databunch)
num_labels = len(databunch.label_names)
if self.train_opts.debug:
make_debug_chips(databunch, self.class_map, tmp_dir, train_uri)
# Setup model
num_labels = len(databunch.label_names)
model = get_model(self.train_opts.model_arch,
num_labels,
pretrained=True)
model = model.to(self.device)
model_path = join(train_dir, 'model')
# Load weights from a pretrained model.
pretrained_uri = self.backend_opts.pretrained_uri
if pretrained_uri:
log.info('Loading weights from pretrained_uri: {}'.format(
pretrained_uri))
pretrained_path = download_if_needed(pretrained_uri, tmp_dir)
model.load_state_dict(
torch.load(pretrained_path, map_location=self.device))
# Possibly resume training from checkpoint.
start_epoch = 0
train_state_path = join(train_dir, 'train_state.json')
if isfile(train_state_path):
log.info('Resuming from checkpoint: {}\n'.format(model_path))
train_state = file_to_json(train_state_path)
start_epoch = train_state['epoch'] + 1
model.load_state_dict(
torch.load(model_path, map_location=self.device))
# Write header of log CSV file.
metric_names = ['precision', 'recall', 'f1']
log_path = join(train_dir, 'log.csv')
if not isfile(log_path):
with open(log_path, 'w') as log_file:
log_writer = csv.writer(log_file)
row = ['epoch', 'time', 'train_loss'] + metric_names
log_writer.writerow(row)
# Setup Tensorboard logging.
if self.train_opts.log_tensorboard:
log_dir = join(train_dir, 'tb-logs')
make_dir(log_dir)
tb_writer = SummaryWriter(log_dir=log_dir)
if self.train_opts.run_tensorboard:
log.info('Starting tensorboard process')
tensorboard_process = Popen(
['tensorboard', '--logdir={}'.format(log_dir)])
terminate_at_exit(tensorboard_process)
# Setup optimizer, loss, and LR scheduler.
loss_fn = torch.nn.CrossEntropyLoss()
lr = self.train_opts.lr
opt = optim.Adam(model.parameters(), lr=lr)
step_scheduler, epoch_scheduler = None, None
num_epochs = self.train_opts.num_epochs
if self.train_opts.one_cycle and num_epochs > 1:
steps_per_epoch = len(databunch.train_ds) // batch_size
total_steps = num_epochs * steps_per_epoch
step_size_up = (num_epochs // 2) * steps_per_epoch
step_size_down = total_steps - step_size_up
step_scheduler = CyclicLR(opt,
base_lr=lr / 10,
max_lr=lr,
step_size_up=step_size_up,
step_size_down=step_size_down,
cycle_momentum=False)
for _ in range(start_epoch * steps_per_epoch):
step_scheduler.step()
# Training loop.
for epoch in range(start_epoch, num_epochs):
# Train one epoch.
log.info('-----------------------------------------------------')
log.info('epoch: {}'.format(epoch))
start = time.time()
train_loss = train_epoch(model, self.device, databunch.train_dl,
opt, loss_fn, step_scheduler)
if epoch_scheduler:
epoch_scheduler.step()
log.info('train loss: {}'.format(train_loss))
# Validate one epoch.
metrics = validate_epoch(model, self.device, databunch.valid_dl,
num_labels)
log.info('validation metrics: {}'.format(metrics))
# Print elapsed time for epoch.
end = time.time()
epoch_time = datetime.timedelta(seconds=end - start)
log.info('epoch elapsed time: {}'.format(epoch_time))
# Save model and state.
torch.save(model.state_dict(), model_path)
train_state = {'epoch': epoch}
json_to_file(train_state, train_state_path)
# Append to log CSV file.
with open(log_path, 'a') as log_file:
log_writer = csv.writer(log_file)
row = [epoch, epoch_time, train_loss]
row += [metrics[k] for k in metric_names]
log_writer.writerow(row)
# Write to Tensorboard log.
if self.train_opts.log_tensorboard:
for key, val in metrics.items():
tb_writer.add_scalar(key, val, epoch)
tb_writer.add_scalar('train_loss', train_loss, epoch)
for name, param in model.named_parameters():
tb_writer.add_histogram(name, param, epoch)
if (train_uri.startswith('s3://')
and (((epoch + 1) % self.train_opts.sync_interval) == 0)):
sync_to_dir(train_dir, train_uri)
# Close Tensorboard.
if self.train_opts.log_tensorboard:
tb_writer.close()
if self.train_opts.run_tensorboard:
tensorboard_process.terminate()
# Since model is exported every epoch, we need some other way to
# show that training is finished.
str_to_file('done!', self.backend_opts.train_done_uri)
# Sync output to cloud.
sync_to_dir(train_dir, self.backend_opts.train_uri)