def common_aug(mode, params):
'''
:param mode: 'train', 'test', 'inference'
:param params:
'''
#aug_params = params.get('augm_params', dict())
augs_list = []
assert mode in {'train', 'debug', 'inference'}
if mode == 'train':
augs_list.append(albumentations.PadIfNeeded(min_height=params.data.net_hw[0], min_width=params.data.net_hw[1],
border_mode=cv2.BORDER_REPLICATE,
always_apply=True))
augs_list.append(albumentations.RandomCrop(height=params.data.net_hw[0], width=params.data.net_hw[1], always_apply=True))
if params.augmentation.rotate_limit:
augs_list.append(T.Rotate(limit=params.augmentation.rotate_limit, border_mode=cv2.BORDER_CONSTANT, always_apply=True))
# augs_list.append(T.OpticalDistortion(border_mode=cv2.BORDER_CONSTANT)) - can't handle boundboxes
elif mode == 'debug':
augs_list.append(albumentations.CenterCrop(height=params.data.net_hw[0], width=params.data.net_hw[1], always_apply=True))
if mode != 'inference':
if params.augmentation.get('blur_limit', 4):
augs_list.append(T.Blur(blur_limit=params.augmentation.get('blur_limit', 4)))
if params.augmentation.get('RandomBrightnessContrast', True):
augs_list.append(T.RandomBrightnessContrast())
#augs_list.append(T.MotionBlur())
if params.augmentation.get('JpegCompression', True):
augs_list.append(T.JpegCompression(quality_lower=30, quality_upper=100))
#augs_list.append(T.VerticalFlip())
if params.augmentation.get('HorizontalFlip', True):
augs_list.append(T.HorizontalFlip())
return albumentations.ReplayCompose(augs_list, p=1., bbox_params = {'format':'albumentations', 'min_visibility':0.5})
def __init__(
self,
prob=0.7,
blur_prob=0.7,
jitter_prob=0.7,
rotate_prob=0.7,
flip_prob=0.7,
):
super().__init__()
self.prob = prob
self.blur_prob = blur_prob
self.jitter_prob = jitter_prob
self.rotate_prob = rotate_prob
self.flip_prob = flip_prob
self.transforms = al.Compose(
[
transforms.RandomRotate90(),
transforms.Flip(),
transforms.HueSaturationValue(),
transforms.RandomBrightnessContrast(),
transforms.Transpose(),
OneOf([
transforms.RandomCrop(220, 220, p=0.5),
transforms.CenterCrop(220, 220, p=0.5)
],
p=0.5),
# transforms.Resize(352,352),
# transforms.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225)),
],
p=self.prob)
def augmentation(mode, target_size, prob=0.5, aug_m=2):
'''
description: augmentation
mode: 'train' 'test'
target_size: int or list, the shape of image ,
aug_m: Strength of transform
'''
high_p = prob
low_p = high_p / 2.0
M = aug_m
first_size = [int(x / 0.7) for x in target_size]
if mode == 'train':
return composition.Compose([
transforms.Resize(first_size[0], first_size[1], interpolation=3),
transforms.Flip(p=0.5),
composition.OneOf([
RandomCenterCut(scale=0.1 * M),
transforms.ShiftScaleRotate(shift_limit=0.05 * M,
scale_limit=0.1 * M,
rotate_limit=180,
border_mode=cv2.BORDER_CONSTANT,
value=0),
albumentations.imgaug.transforms.IAAAffine(
shear=(-10 * M, 10 * M), mode='constant')
],
p=high_p),
transforms.RandomBrightnessContrast(
brightness_limit=0.1 * M, contrast_limit=0.03 * M, p=high_p),
transforms.HueSaturationValue(hue_shift_limit=5 * M,
sat_shift_limit=15 * M,
val_shift_limit=10 * M,
p=high_p),
transforms.OpticalDistortion(distort_limit=0.03 * M,
shift_limit=0,
border_mode=cv2.BORDER_CONSTANT,
value=0,
p=low_p),
composition.OneOf([
transforms.Blur(blur_limit=7),
albumentations.imgaug.transforms.IAASharpen(),
transforms.GaussNoise(var_limit=(2.0, 10.0), mean=0),
transforms.ISONoise()
],
p=low_p),
transforms.Resize(target_size[0], target_size[1], interpolation=3),
transforms.Normalize(mean=(0.5, 0.5, 0.5),
std=(0.5, 0.5, 0.5),
max_pixel_value=255.0)
],
p=1)
else:
return composition.Compose([
transforms.Resize(target_size[0], target_size[1], interpolation=3),
transforms.Normalize(mean=(0.5, 0.5, 0.5),
std=(0.5, 0.5, 0.5),
max_pixel_value=255.0)
],
p=1)
def RandomBrightnessContrast(brightness_limit=0.2,
contrast_limit=0.2,
brightness_by_max=True,
p=0.5):
return transforms.RandomBrightnessContrast(
brightness_limit=brightness_limit,
contrast_limit=contrast_limit,
brightness_by_max=brightness_by_max,
p=p)
def get_presize_combine_transforms_V4():
transforms_presize = A.Compose([
transforms.PadIfNeeded(600, 800),
geometric.Perspective(
scale=[0, .1],
pad_mode=cv2.BORDER_REFLECT,
interpolation=cv2.INTER_AREA, p = .3),
transforms.Flip(),
geometric.ShiftScaleRotate(interpolation=cv2.INTER_LANCZOS4, p = 0.95, scale_limit=0.0),
crops.RandomResizedCrop(
TARGET_SIZE, TARGET_SIZE,
scale=(config['rrc_scale_min'], config['rrc_scale_max']),
ratio=(.70, 1.4),
interpolation=cv2.INTER_CUBIC,
p=1.0),
transforms.Transpose()
#rotate.Rotate(interpolation=cv2.INTER_LANCZOS4, p = 0.99),
])
transforms_postsize = A.Compose([
#imgaug.IAAPiecewiseAffine(),
transforms.CoarseDropout(),
transforms.CLAHE(p=.1),
transforms.RandomToneCurve(scale=.1, p=0.2),
transforms.RandomBrightnessContrast(
brightness_limit=.1,
contrast_limit=0.4,
p=.8),
transforms.HueSaturationValue(
hue_shift_limit=20,
sat_shift_limit=50,
val_shift_limit=0,
p=0.5),
transforms.Equalize(p=0.05),
transforms.FancyPCA(p=0.05),
transforms.RandomGridShuffle(p=0.1),
A.OneOf([
transforms.MotionBlur(blur_limit=(3, 9)),
transforms.GaussianBlur(),
transforms.MedianBlur()
], p=0.1),
transforms.ISONoise(p=.2),
transforms.GaussNoise(var_limit=127., p=.3),
A.OneOf([
transforms.GridDistortion(interpolation=cv2.INTER_AREA, distort_limit=[0.7, 0.7], p=0.5),
transforms.OpticalDistortion(interpolation=cv2.INTER_AREA, p=.3),
], p=.3),
geometric.ElasticTransform(alpha=4, sigma=4, alpha_affine=4, interpolation=cv2.INTER_AREA, p=0.3),
transforms.CoarseDropout(),
transforms.Normalize(),
ToTensorV2()
])
return transforms_presize, transforms_postsize
def __init__(self, brightness_coeff: float = -1) -> None:
"""
Initialize the brightener
:param brightness_coeff: coefficient between 0 and 1 that controls brightness,
if brightness_coeff is -1, the value is drawn from uniform distribution on [0.0, 1.0) upon each application
"""
self.brightness_coeff = brightness_coeff
brightness_coeff_lower, brightness_coeff_upper = brightness_coeff, brightness_coeff
if self.brightness_coeff == -1:
brightness_coeff_lower, brightness_coeff_upper = 0.0, 1.0
self.brighten_object = albu.RandomBrightnessContrast(
(brightness_coeff_lower, brightness_coeff_upper), (0.0, 0.0),
always_apply=True)
def get_presize_combine_tune_transforms():
transforms_presize = A.Compose([
transforms.Transpose(),
transforms.Flip(),
#transforms.PadIfNeeded(600, 800),
crops.RandomResizedCrop(
TARGET_SIZE, TARGET_SIZE,
scale=(.75, 1),
interpolation=cv2.INTER_CUBIC,
p=1.0),
rotate.Rotate(interpolation=cv2.INTER_LANCZOS4, p = 0.99),
])
transforms_postsize = A.Compose([
transforms.CoarseDropout(),
# transforms.CLAHE(p=.1),
transforms.RandomToneCurve(scale=.1),
transforms.RandomBrightnessContrast(
brightness_limit=.1,
contrast_limit=0.2,
p=.7),
transforms.HueSaturationValue(
hue_shift_limit=20,
sat_shift_limit=60,
val_shift_limit=0,
p=0.6),
#transforms.Equalize(p=0.1),
#transforms.FancyPCA(p=0.05),
#transforms.RandomGridShuffle(p=0.1),
#A.OneOf([
# transforms.MotionBlur(blur_limit=(3, 9)),
# transforms.GaussianBlur(),
# transforms.MedianBlur()
# ], p=0.2),
transforms.ISONoise(p=.3),
transforms.GaussNoise(var_limit=255., p=.3),
#A.OneOf([
# transforms.GridDistortion(interpolation=cv2.INTER_AREA, distort_limit=[0.7, 0.7], p=0.5),
# transforms.OpticalDistortion(interpolation=cv2.INTER_AREA, p=.3),
# ], p=.3),
geometric.ElasticTransform(alpha=4, sigma=100, alpha_affine=100, interpolation=cv2.INTER_AREA, p=0.3),
transforms.CoarseDropout(),
transforms.Normalize(),
ToTensorV2()
])
return transforms_presize, transforms_postsize
def get_augmentations():
"""Get a list of 'major' and 'minor' augmentation functions for the pipeline in a dictionary."""
return {
"major": {
"shift-scale-rot":
trans.ShiftScaleRotate(
shift_limit=0.05,
rotate_limit=35,
border_mode=cv2.BORDER_REPLICATE,
always_apply=True,
),
"crop":
trans.RandomResizedCrop(100,
100,
scale=(0.8, 0.95),
ratio=(0.8, 1.2),
always_apply=True),
# "elastic": trans.ElasticTransform(
# alpha=0.8,
# alpha_affine=10,
# sigma=40,
# border_mode=cv2.BORDER_REPLICATE,
# always_apply=True,
# ),
"distort":
trans.OpticalDistortion(0.2, always_apply=True),
},
"minor": {
"blur":
trans.GaussianBlur(7, always_apply=True),
"noise":
trans.GaussNoise((20.0, 40.0), always_apply=True),
"bright-contrast":
trans.RandomBrightnessContrast(0.4, 0.4, always_apply=True),
"hsv":
trans.HueSaturationValue(30, 40, 50, always_apply=True),
"rgb":
trans.RGBShift(always_apply=True),
"flip":
trans.HorizontalFlip(always_apply=True),
},
}
def get_train_transforms():
return A.Compose([
transforms.PadIfNeeded(600, 800),
geometric.ShiftScaleRotate(interpolation=cv2.INTER_LANCZOS4, p = 0.99, scale_limit=0.8),
geometric.Perspective(pad_mode=cv2.BORDER_REFLECT,interpolation=cv2.INTER_AREA),
crops.RandomResizedCrop(
TARGET_SIZE, TARGET_SIZE,
scale=(config['rrc_scale_min'], config['rrc_scale_max']),
interpolation=cv2.INTER_CUBIC,
p=1.0),
transforms.Transpose(),
transforms.Flip(),
transforms.CoarseDropout(),
transforms.CLAHE(p=.1),
transforms.RandomToneCurve(scale=.1),
transforms.RandomBrightnessContrast(
brightness_limit=.1,
contrast_limit=0.3,
p=.7),
transforms.HueSaturationValue(
hue_shift_limit=20,
sat_shift_limit=60,
val_shift_limit=0,
p=0.6),
transforms.RandomGridShuffle(p=0.1),
A.OneOf([
transforms.MotionBlur(blur_limit=(3, 9)),
transforms.GaussianBlur(),
transforms.MedianBlur()
], p=0.2),
transforms.ISONoise(p=.3),
transforms.GaussNoise(var_limit=255., p=.3),
A.OneOf([
transforms.GridDistortion(interpolation=cv2.INTER_AREA, distort_limit=[0.7, 0.7], p=0.5),
transforms.OpticalDistortion(interpolation=cv2.INTER_AREA, p=.3),
], p=.3),
geometric.ElasticTransform(alpha=4, sigma=100, alpha_affine=100, interpolation=cv2.INTER_AREA, p=0.3),
transforms.CoarseDropout(),
transforms.Normalize(),
ToTensorV2()
])
def train_dataloader(self):
augmentations = Compose(
[
A.RandomResizedCrop(
height=self.hparams.sz,
width=self.hparams.sz,
scale=(0.7, 1.0),
),
# AdvancedHairAugmentation(),
A.GridDistortion(),
A.RandomBrightnessContrast(),
A.ShiftScaleRotate(),
A.Flip(p=0.5),
A.CoarseDropout(
max_height=int(self.hparams.sz / 10),
max_width=int(self.hparams.sz / 10),
),
# A.HueSaturationValue(),
A.Normalize(
mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225],
max_pixel_value=255,
),
ToTensorV2(),
]
)
train_ds = MelanomaDataset(
df=self.train_df,
images_path=self.train_images_path,
augmentations=augmentations,
train_or_valid=True,
)
return DataLoader(
train_ds,
# sampler=sampler,
batch_size=self.hparams.bs,
shuffle=True,
num_workers=os.cpu_count(),
pin_memory=True,
)
def get_tta_transforms():
return Compose([
A.RandomResizedCrop(
height=hparams.sz,
width=hparams.sz,
scale=(0.7, 1.0),
),
# AdvancedHairAugmentation(),
A.GridDistortion(),
A.RandomBrightnessContrast(),
A.ShiftScaleRotate(),
A.Flip(p=0.5),
A.CoarseDropout(
max_height=int(hparams.sz / 10),
max_width=int(hparams.sz / 10),
),
# A.HueSaturationValue(),
A.Normalize(
mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225],
max_pixel_value=255,
),
ToTensorV2(),
])
train_img_paths = []
train_mask_paths = []
train_data_path = ["data/kvasir-seg/TrainDataset"]
for i in train_data_path:
train_img_paths.extend(glob(os.path.join(i, "images", "*")))
train_mask_paths.extend(glob(os.path.join(i, "masks", "*")))
train_img_paths.sort()
train_mask_paths.sort()
transforms = al.Compose(
[
transforms.RandomRotate90(),
transforms.Flip(),
transforms.HueSaturationValue(),
transforms.RandomBrightnessContrast(),
transforms.Transpose(),
OneOf(
[
transforms.RandomCrop(220, 220, p=0.5),
transforms.CenterCrop(220, 220, p=0.5),
],
p=1,
),
# transforms.Resize(352,352),
# transforms.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225)),
],
p=1,
)
dataset = KvasirDataset(train_img_paths,
train_mask_paths,
def main():
# config = vars(parse_args_func())
#config_file = "../configs/config_v1.json"
args = vars(parse_args_func())
config_file = args['config']
config_dict = json.loads(open(config_file, 'rt').read())
# config_dict = json.loads(open(sys.argv[1], 'rt').read())
file_dict = config_dict['file_path']
config = config_dict['opt_config']
input_folder = file_dict['input_path'] # '../inputs'
checkpoint_folder = file_dict['checkpoint_path'] # '../checkpoint'
model_folder = file_dict['model_path'] # '../models'
if 'False' in config['deep_supervision']:
config['deep_supervision'] = False
else:
config['deep_supervision'] = True
if 'False' in config['nesterov']:
config['nesterov'] = False
else:
config['nesterov'] = True
if 'None' in config['name']:
config['name'] = None
if config['name'] is None:
config['name'] = '%s_%s_segmodel' % (config['dataset'], config['arch'])
os.makedirs(os.path.join(model_folder, '%s' % config['name']),
exist_ok=True)
print('-' * 20)
for key in config:
print('%s: %s' % (key, config[key]))
print('-' * 20)
with open(os.path.join(model_folder, '%s/config.yml' % config['name']),
'w') as f:
yaml.dump(config, f)
# define loss function (criterion)
if config['loss'] == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[config['loss']]().cuda()
cudnn.benchmark = True
# create model
if 'False' in config['resume']:
config['resume'] = False
else:
config['resume'] = True
# Data loading code
img_ids = glob(
os.path.join(input_folder, config['dataset'], 'images', 'training',
'*' + config['img_ext']))
train_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
img_ids = glob(
os.path.join(input_folder, config['val_dataset'], 'images',
'validation', '*' + config['img_ext']))
val_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
img_ids = glob(
os.path.join(input_folder, config['val_dataset'], 'images', 'test',
'*' + config['img_ext']))
test_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
mean = [0.485, 0.456, 0.406]
std = [0.229, 0.224, 0.225]
train_transform = Compose([
# transforms.RandomScale ([config['scale_min'], config['scale_max']]),
# transforms.RandomRotate90(),
transforms.Rotate([config['rotate_min'], config['rotate_max']],
value=mean,
mask_value=0),
# transforms.GaussianBlur (),
transforms.Flip(),
# transforms.HorizontalFlip (),
transforms.HueSaturationValue(hue_shift_limit=10,
sat_shift_limit=10,
val_shift_limit=10),
transforms.RandomBrightnessContrast(brightness_limit=0.10,
contrast_limit=0.10,
brightness_by_max=True),
transforms.Resize(config['input_h'], config['input_w']),
transforms.Normalize(mean=mean, std=std),
])
val_transform = Compose([
transforms.Resize(config['input_h'], config['input_w']),
transforms.Normalize(mean=mean, std=std),
])
train_dataset = Dataset(img_ids=train_img_ids,
img_dir=os.path.join(input_folder,
config['dataset'], 'images',
'training'),
mask_dir=os.path.join(input_folder,
config['dataset'],
'annotations', 'training'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=train_transform)
val_dataset = Dataset(img_ids=val_img_ids,
img_dir=os.path.join(input_folder, config['dataset'],
'images', 'validation'),
mask_dir=os.path.join(input_folder,
config['dataset'],
'annotations', 'validation'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=val_transform)
test_dataset = Dataset(img_ids=val_img_ids,
img_dir=os.path.join(input_folder,
config['dataset'], 'images',
'test'),
mask_dir=os.path.join(input_folder,
config['dataset'],
'annotations', 'test'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=val_transform)
train_loader = torch.utils.data.DataLoader(
train_dataset,
batch_size=config['batch_size'],
shuffle=True,
num_workers=config['num_workers'],
drop_last=True)
val_loader = torch.utils.data.DataLoader(
val_dataset,
batch_size=1, # config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
drop_last=False)
test_loader = torch.utils.data.DataLoader(
test_dataset,
batch_size=1, # config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
drop_last=False)
log = OrderedDict([
('epoch', []),
('lr', []),
('loss', []),
('iou', []),
('dice', []),
('val_loss', []),
('val_iou', []),
('val_dice', []),
])
if not os.path.isdir(checkpoint_folder):
os.mkdir(checkpoint_folder)
# create generator model
#val_config = config_dict['config']
generator_name = config['generator_name']
with open(os.path.join(model_folder, '%s/config.yml' % generator_name),
'r') as f:
g_config = yaml.load(f, Loader=yaml.FullLoader)
generator = Generator(g_config)
generator.initialize_with_srresnet(model_folder, g_config)
lr = config['gan_lr']
# Initialize generator's optimizer
optimizer_g = torch.optim.Adam(params=filter(lambda p: p.requires_grad,
generator.parameters()),
lr=lr)
#params = filter(lambda p: p.requires_grad, generator.parameters())
#optimizer_g, scheduler_g = optimizer_scheduler(params, config)
# Discriminator
# Discriminator parameters
num_classes = config['num_classes']
kernel_size_d = 3 # kernel size in all convolutional blocks
n_channels_d = 64 # number of output channels in the first convolutional block, after which it is doubled in every 2nd block thereafter
n_blocks_d = 8 # number of convolutional blocks
fc_size_d = 1024 # size of the first fully connected layer
discriminator = Discriminator(num_classes,
kernel_size=kernel_size_d,
n_channels=n_channels_d,
n_blocks=n_blocks_d,
fc_size=fc_size_d)
# Initialize discriminator's optimizer
optimizer_d = torch.optim.Adam(params=filter(lambda p: p.requires_grad,
discriminator.parameters()),
lr=lr)
#params = filter(lambda p: p.requires_grad, discriminator.parameters())
#optimizer_d, scheduler_d = optimizer_scheduler(params, config)
adversarial_loss_criterion = nn.BCEWithLogitsLoss()
content_loss_criterion = nn.MSELoss()
generator = generator.cuda()
discriminator = discriminator.cuda()
#truncated_vgg19 = truncated_vgg19.cuda()
content_loss_criterion = content_loss_criterion.cuda()
adversarial_loss_criterion = adversarial_loss_criterion.cuda()
generator = torch.nn.DataParallel(generator)
discriminator = torch.nn.DataParallel(discriminator)
if not os.path.isdir(checkpoint_folder):
os.mkdir(checkpoint_folder)
log_name = config['name']
log_dir = os.path.join(checkpoint_folder, log_name)
writer = SummaryWriter(logdir=log_dir)
best_iou = 0
trigger = 0
Best_dice = 0
iou_AtBestDice = 0
start_epoch = 0
for epoch in range(start_epoch, config['epochs']):
print('Epoch [%d/%d]' % (epoch, config['epochs']))
# train for one epoch
train_log = train(epoch, config, train_loader, generator,
discriminator, criterion, adversarial_loss_criterion,
content_loss_criterion, optimizer_g, optimizer_d)
# evaluate on validation set
val_log = validate(config, val_loader, generator, criterion)
test_log = validate(config, test_loader, generator, criterion)
if Best_dice < test_log['dice']:
Best_dice = test_log['dice']
iou_AtBestDice = test_log['iou']
print(
'loss %.4f - iou %.4f - dice %.4f - val_loss %.4f - val_iou %.4f - val_dice %.4f - test_iou %.4f - test_dice %.4f - Best_dice %.4f - iou_AtBestDice %.4f'
% (train_log['loss'], train_log['iou'], train_log['dice'],
val_log['loss'], val_log['iou'], val_log['dice'],
test_log['iou'], test_log['dice'], Best_dice, iou_AtBestDice))
save_tensorboard(writer, train_log, val_log, test_log, epoch)
log['epoch'].append(epoch)
log['lr'].append(config['lr'])
log['loss'].append(train_log['loss'])
log['iou'].append(train_log['iou'])
log['dice'].append(train_log['dice'])
log['val_loss'].append(val_log['loss'])
log['val_iou'].append(val_log['iou'])
log['val_dice'].append(val_log['dice'])
pd.DataFrame(log).to_csv(os.path.join(model_folder,
'%s/log.csv' % config['name']),
index=False)
trigger += 1
if test_log['iou'] > best_iou:
torch.save(
generator.state_dict(),
os.path.join(model_folder, '%s/model.pth' % config['name']))
best_iou = test_log['iou']
print("=> saved best model")
trigger = 0
# early stopping
if config['early_stopping'] >= 0 and trigger >= config[
'early_stopping']:
print("=> early stopping")
break
torch.cuda.empty_cache()
# axs[0].imshow(image)
# axs[0].set_title("Original",fontsize=30)
# image_ = transforms.RandomRotate90(always_apply=True)(image=image)["image"]
# axs[1].imshow(image_)
# axs[1].set_title("Rotate",fontsize=30)
# image_ = transforms.Flip(always_apply=True)(image=image)["image"]
# axs[2].imshow(image_)
# axs[2].set_title("Flip",fontsize=30)
image_ = transforms.HueSaturationValue(always_apply=True)(image=image)["image"]
axs[0].imshow(image_)
axs[0].set_title("Saturation", fontsize=30)
image_ = transforms.RandomBrightnessContrast(always_apply=True)(
image=image)["image"]
axs[1].imshow(image_)
axs[1].set_title("Brightness", fontsize=30)
image_ = OneOf(
[
transforms.RandomCrop(204, 250, p=1),
transforms.CenterCrop(204, 250, p=1),
],
p=1,
)(image=image)["image"]
axs[2].imshow(image_)
axs[2].set_title("Random Crop", fontsize=30)
def augment(im, params=None):
"""
Perform data augmentation on some image using the albumentations package.
Parameters
----------
im : Numpy array
params : dict or None
Contains the data augmentation parameters
Mandatory keys:
- h_flip ([0,1] float): probability of performing an horizontal left-right mirroring.
- v_flip ([0,1] float): probability of performing an vertical up-down mirroring.
- rot ([0,1] float): probability of performing a rotation to the image.
- rot_lim (int): max degrees of rotation.
- stretch ([0,1] float): probability of randomly stretching an image.
- crop ([0,1] float): randomly take an image crop.
- zoom ([0,1] float): random zoom applied to crop_size.
--> Therefore the effective crop size at each iteration will be a
random number between 1 and crop*(1-zoom). For example:
* crop=1, zoom=0: no crop of the image
* crop=1, zoom=0.1: random crop of random size between 100% image and 90% of the image
* crop=0.9, zoom=0.1: random crop of random size between 90% image and 80% of the image
* crop=0.9, zoom=0: random crop of always 90% of the image
Image size refers to the size of the shortest side.
- blur ([0,1] float): probability of randomly blurring an image.
- pixel_noise ([0,1] float): probability of randomly adding pixel noise to an image.
- pixel_sat ([0,1] float): probability of randomly using HueSaturationValue in the image.
- cutout ([0,1] float): probability of using cutout in the image.
Returns
-------
Numpy array
"""
## 1) Crop the image
effective_zoom = np.random.rand() * params['zoom']
crop = params['crop'] - effective_zoom
ly, lx, channels = im.shape
crop_size = int(crop * min([ly, lx]))
rand_x = np.random.randint(low=0, high=lx - crop_size + 1)
rand_y = np.random.randint(low=0, high=ly - crop_size + 1)
crop = transforms.Crop(x_min=rand_x,
y_min=rand_y,
x_max=rand_x + crop_size,
y_max=rand_y + crop_size)
im = crop(image=im)['image']
## 2) Now add the transformations for augmenting the image pixels
transform_list = []
# Add random stretching
if params['stretch']:
transform_list.append(
imgaug_transforms.IAAPerspective(scale=0.1, p=params['stretch']))
# Add random rotation
if params['rot']:
transform_list.append(
transforms.Rotate(limit=params['rot_lim'], p=params['rot']))
# Add horizontal flip
if params['h_flip']:
transform_list.append(transforms.HorizontalFlip(p=params['h_flip']))
# Add vertical flip
if params['v_flip']:
transform_list.append(transforms.VerticalFlip(p=params['v_flip']))
# Add some blur to the image
if params['blur']:
transform_list.append(
albumentations.OneOf([
transforms.MotionBlur(blur_limit=7, p=1.),
transforms.MedianBlur(blur_limit=7, p=1.),
transforms.Blur(blur_limit=7, p=1.),
],
p=params['blur']))
# Add pixel noise
if params['pixel_noise']:
transform_list.append(
albumentations.OneOf(
[
transforms.CLAHE(clip_limit=2, p=1.),
imgaug_transforms.IAASharpen(p=1.),
imgaug_transforms.IAAEmboss(p=1.),
transforms.RandomBrightnessContrast(contrast_limit=0,
p=1.),
transforms.RandomBrightnessContrast(brightness_limit=0,
p=1.),
transforms.RGBShift(p=1.),
transforms.RandomGamma(p=1.) #,
# transforms.JpegCompression(),
# transforms.ChannelShuffle(),
# transforms.ToGray()
],
p=params['pixel_noise']))
# Add pixel saturation
if params['pixel_sat']:
transform_list.append(
transforms.HueSaturationValue(p=params['pixel_sat']))
# Remove randomly remove some regions from the image
if params['cutout']:
ly, lx, channels = im.shape
scale_low, scale_high = 0.05, 0.25 # min and max size of the squares wrt the full image
scale = np.random.uniform(scale_low, scale_high)
transform_list.append(
transforms.Cutout(num_holes=8,
max_h_size=int(scale * ly),
max_w_size=int(scale * lx),
p=params['cutout']))
# Compose all image transformations and augment the image
augmentation_fn = albumentations.Compose(transform_list)
im = augmentation_fn(image=im)['image']
return im
def augment(im, params=None):
"""
Perform data augmentation on some image using the albumentations package.
Parameters
----------
im : Numpy array
params : dict or None
Contains the data augmentation parameters
Mandatory keys:
- h_flip ([0,1] float): probability of performing an horizontal left-right mirroring.
- v_flip ([0,1] float): probability of performing an vertical up-down mirroring.
- rot ([0,1] float): probability of performing a rotation to the image.
- rot_lim (int): max degrees of rotation.
- stretch ([0,1] float): probability of randomly stretching an image.
- expand ([True, False] bool): whether to pad the image to a square shape with background color canvas.
- crop ([0,1] float): randomly take an image crop.
- invert_col ([0, 1] float): randomly invert the colors of the image. p=1 -> invert colors (VPR)
- zoom ([0,1] float): random zoom applied to crop_size.
--> Therefore the effective crop size at each iteration will be a
random number between 1 and crop*(1-zoom). For example:
* crop=1, zoom=0: no crop of the image
* crop=1, zoom=0.1: random crop of random size between 100% image and 90% of the image
* crop=0.9, zoom=0.1: random crop of random size between 90% image and 80% of the image
* crop=0.9, zoom=0: random crop of always 90% of the image
Image size refers to the size of the shortest side.
- blur ([0,1] float): probability of randomly blurring an image.
- pixel_noise ([0,1] float): probability of randomly adding pixel noise to an image.
- pixel_sat ([0,1] float): probability of randomly using HueSaturationValue in the image.
- cutout ([0,1] float): probability of using cutout in the image.
Returns
-------
Numpy array
"""
## 1) Expand the image by padding it with bg-color canvas
if params["expand"]:
desired_size = max(im.shape)
# check bg
if np.argmax(im.shape) > 0:
bgcol = tuple(np.repeat(int(np.mean(im[[0, -1], :, :])), 3))
else:
bgcol = tuple(np.repeat(int(np.mean(im[:, [0, -1], :])), 3))
im = Image.fromarray(im)
old_size = im.size # old_size[0] is in (width, height) format
ratio = float(desired_size) / max(old_size)
new_size = tuple([int(x * ratio) for x in old_size])
im = im.resize(new_size, Image.ANTIALIAS)
# create a new image and paste the resized on it
new_im = Image.new("RGB", (desired_size, desired_size), color=bgcol)
new_im.paste(im, ((desired_size - new_size[0]) // 2,
(desired_size - new_size[1]) // 2))
im = np.array(new_im)
## 2) Crop the image
if params["crop"] and params["crop"] != 1:
effective_zoom = np.random.rand() * params['zoom']
crop = params['crop'] - effective_zoom
ly, lx, channels = im.shape
crop_size = int(crop * min([ly, lx]))
rand_x = np.random.randint(low=0, high=lx - crop_size + 1)
rand_y = np.random.randint(low=0, high=ly - crop_size + 1)
crop = transforms.Crop(x_min=rand_x,
y_min=rand_y,
x_max=rand_x + crop_size,
y_max=rand_y + crop_size)
im = crop(image=im)['image']
if params["enhance"]:
im = Image.fromarray(im)
enhancer = ImageEnhance.Contrast(im)
im = np.array(enhancer.enhance(params["enhance"]))
## 3) Now add the transformations for augmenting the image pixels
transform_list = []
if params['invert_col']:
transform_list.append(transforms.InvertImg(p=params['invert_col']))
# Add random stretching
if params['stretch']:
transform_list.append(
imgaug_transforms.IAAPerspective(scale=0.1, p=params['stretch']))
# Add random rotation
if params['rot']:
transform_list.append(
transforms.Rotate(limit=params['rot_lim'], p=params['rot']))
# Add horizontal flip
if params['h_flip']:
transform_list.append(transforms.HorizontalFlip(p=params['h_flip']))
# Add vertical flip
if params['v_flip']:
transform_list.append(transforms.VerticalFlip(p=params['v_flip']))
# Add some blur to the image
if params['blur']:
transform_list.append(
albumentations.OneOf([
transforms.MotionBlur(blur_limit=7, p=1.),
transforms.MedianBlur(blur_limit=7, p=1.),
transforms.Blur(blur_limit=7, p=1.),
],
p=params['blur']))
# Add pixel noise
if params['pixel_noise']:
transform_list.append(
albumentations.OneOf(
[
transforms.CLAHE(clip_limit=2, p=1.),
imgaug_transforms.IAASharpen(p=1.),
imgaug_transforms.IAAEmboss(p=1.),
transforms.RandomBrightnessContrast(contrast_limit=0,
p=1.),
transforms.RandomBrightnessContrast(brightness_limit=0,
p=1.),
transforms.RGBShift(p=1.),
transforms.RandomGamma(p=1.) #,
# transforms.JpegCompression(),
# transforms.ChannelShuffle(),
# transforms.ToGray()
],
p=params['pixel_noise']))
# Add pixel saturation
if params['pixel_sat']:
transform_list.append(
transforms.HueSaturationValue(p=params['pixel_sat']))
# Remove randomly remove some regions from the image
if params['cutout']:
ly, lx, channels = im.shape
scale_low, scale_high = 0.05, 0.25 # min and max size of the squares wrt the full image
scale = np.random.uniform(scale_low, scale_high)
transform_list.append(
transforms.Cutout(num_holes=8,
max_h_size=int(scale * ly),
max_w_size=int(scale * lx),
p=params['cutout']))
# Compose all image transformations and augment the image
augmentation_fn = albumentations.Compose(transform_list)
im = augmentation_fn(image=im)['image']
return im
alb_transforms = [
alb.IAAAdditiveGaussianNoise(p=1),
alb.GaussNoise(p=1),
alb.MotionBlur(p=1),
alb.MedianBlur(blur_limit=3, p=1),
alb.Blur(blur_limit=3, p=1),
alb.OpticalDistortion(p=1),
alb.GridDistortion(p=1),
alb.IAAPiecewiseAffine(p=1),
aat.CLAHE(clip_limit=2, p=1),
alb.IAASharpen(p=1),
alb.IAAEmboss(p=1),
aat.HueSaturationValue(p=0.3),
aat.HorizontalFlip(p=1),
aat.RGBShift(),
aat.RandomBrightnessContrast(),
aat.RandomGamma(p=1),
aat.Cutout(2, 10, 10, p=1),
aat.Equalize(mode='cv', p=1),
aat.FancyPCA(p=1),
aat.RandomFog(p=1),
aat.RandomRain(blur_value=3, p=1),
albumentations.IAAAffine(p=1),
albumentations.ShiftScaleRotate(rotate_limit=15, p=1)
]
def one_by_one():
data_dir = 'train_val/pic'
data_anno = pd.read_csv('train_val/keys.csv')
orig = MyDataset(data_dir, data_anno)
def __init__(
self,
prob=0,
Flip_prob=0,
HueSaturationValue_prob=0,
RandomBrightnessContrast_prob=0,
crop_prob=0,
randomrotate90_prob=0,
elastictransform_prob=0,
gridistortion_prob=0,
opticaldistortion_prob=0,
verticalflip_prob=0,
horizontalflip_prob=0,
randomgamma_prob=0,
CoarseDropout_prob=0,
RGBShift_prob=0,
MotionBlur_prob=0,
MedianBlur_prob=0,
GaussianBlur_prob=0,
GaussNoise_prob=0,
ChannelShuffle_prob=0,
ColorJitter_prob=0,
):
super().__init__()
self.prob = prob
self.randomrotate90_prob = randomrotate90_prob
self.elastictransform_prob = elastictransform_prob
self.transforms = al.Compose(
[
transforms.RandomRotate90(p=randomrotate90_prob),
transforms.Flip(p=Flip_prob),
transforms.HueSaturationValue(p=HueSaturationValue_prob),
transforms.RandomBrightnessContrast(
p=RandomBrightnessContrast_prob),
transforms.Transpose(),
OneOf(
[
transforms.RandomCrop(220, 220, p=0.5),
transforms.CenterCrop(220, 220, p=0.5),
],
p=crop_prob,
),
ElasticTransform(
p=elastictransform_prob,
alpha=120,
sigma=120 * 0.05,
alpha_affine=120 * 0.03,
),
GridDistortion(p=gridistortion_prob),
OpticalDistortion(p=opticaldistortion_prob,
distort_limit=2,
shift_limit=0.5),
VerticalFlip(p=verticalflip_prob),
HorizontalFlip(p=horizontalflip_prob),
RandomGamma(p=randomgamma_prob),
RGBShift(p=RGBShift_prob),
MotionBlur(p=MotionBlur_prob, blur_limit=7),
MedianBlur(p=MedianBlur_prob, blur_limit=9),
GaussianBlur(p=GaussianBlur_prob, blur_limit=9),
GaussNoise(p=GaussNoise_prob),
ChannelShuffle(p=ChannelShuffle_prob),
CoarseDropout(p=CoarseDropout_prob,
max_holes=8,
max_height=32,
max_width=32),
ColorJitter(p=ColorJitter_prob)
# transforms.Resize(352, 352),
# transforms.Normalize(
# mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225)
# ),
],
p=self.prob,
)
def get_transforms(phase: str, cli_args) -> Dict[str, Compose]:
"""Get composed albumentations augmentations
Parameters
----------
phase : str
Phase of learning
In ['train', 'val']
cli_args
Arguments coming all the way from `main.py`
Returns
-------
transforms: dict[str, albumentations.core.composition.Compose]
Composed list of transforms
"""
aug_transforms = []
im_sz = (cli_args.image_size, cli_args.image_size)
if phase == "train":
# Data augmentation for training only
aug_transforms.extend([
tf.ShiftScaleRotate(
shift_limit=0,
scale_limit=0.1,
rotate_limit=15,
p=0.5),
tf.Flip(p=0.5),
tf.RandomRotate90(p=0.5),
])
# Exotic Augmentations for train only 🤤
aug_transforms.extend([
tf.RandomBrightnessContrast(p=0.5),
tf.ElasticTransform(p=0.5),
tf.MultiplicativeNoise(multiplier=(0.5, 1.5),
per_channel=True, p=0.2),
])
aug_transforms.extend([
tf.RandomSizedCrop(min_max_height=im_sz,
height=im_sz[0],
width=im_sz[1],
w2h_ratio=1.0,
interpolation=cv2.INTER_LINEAR,
p=1.0),
])
aug_transforms = Compose(aug_transforms)
mask_only_transforms = Compose([
tf.Normalize(mean=0, std=1, always_apply=True)
])
image_only_transforms = Compose([
tf.Normalize(mean=(0.0, 0.0, 0.0), std=(1.0, 1.0, 1.0),
always_apply=True)
])
final_transforms = Compose([
ToTensorV2()
])
transforms = {
'aug': aug_transforms,
'img_only': image_only_transforms,
'mask_only': mask_only_transforms,
'final': final_transforms
}
return transforms
def __init__(self) -> None:
"""
Initializes the random brightener/darkener
"""
self.darken_or_brighten_object = albu.RandomBrightnessContrast(
(-1.0, 1.0), (0.0, 0.0), always_apply=True)
def main():
args = vars(parse_args_func())
#config_file = "../configs/config_SN7.json"
config_file = args['config'] # "../configs/config_v1.json"
config_dict = json.loads(open(config_file, 'rt').read())
#config_dict = json.loads(open(sys.argv[1], 'rt').read())
file_dict = config_dict['file_path']
config = config_dict['opt_config']
input_folder = file_dict['input_path'] # '../inputs'
checkpoint_folder = file_dict['checkpoint_path'] # '../checkpoint'
model_folder = file_dict['model_path'] # '../models'
if 'False' in config['deep_supervision']:
config['deep_supervision'] = False
else:
config['deep_supervision'] = True
if 'False' in config['nesterov']:
config['nesterov'] = False
else:
config['nesterov'] = True
if 'None' in config['name']:
config['name'] = None
if config['name'] is None:
config['name'] = '%s_%s_segmodel' % (config['dataset'], config['arch'])
os.makedirs(os.path.join(model_folder, '%s' % config['name']),
exist_ok=True)
if not os.path.isdir(checkpoint_folder):
os.mkdir(checkpoint_folder)
log_name = config['name']
log_dir = os.path.join(checkpoint_folder, log_name)
writer = SummaryWriter(logdir=log_dir)
print('-' * 20)
for key in config:
print('%s: %s' % (key, config[key]))
print('-' * 20)
with open(os.path.join(model_folder, '%s/config.yml' % config['name']),
'w') as f:
yaml.dump(config, f)
# define loss function (criterion)
if config['loss'] == 'BCEWithLogitsLoss':
criterion = nn.BCEWithLogitsLoss().cuda()
else:
criterion = losses.__dict__[config['loss']]().cuda()
cudnn.benchmark = True
# create model
print("=> creating model %s" % config['arch'])
model = archs.__dict__[config['arch']](config['num_classes'],
config['input_channels'],
config['deep_supervision'])
if 'False' in config['resume']:
config['resume'] = False
else:
config['resume'] = True
resume_flag = False
if resume_flag == True:
save_path = os.path.join(model_folder, config['name'], 'model.pth')
weights = torch.load(save_path)
model.load_state_dict(weights)
name_yaml = config['name']
with open(os.path.join(model_folder, '%s/config.yml' % name_yaml),
'r') as f:
config = yaml.load(f, Loader=yaml.FullLoader)
#start_epoch = config['epochs']
start_epoch = 0
else:
start_epoch = 0
model = model.cuda()
if 'effnet' in config['arch']:
eff_flag = True
else:
eff_flag = False
if eff_flag == True:
cnn_subs = list(model.encoder.eff_conv.children())[1:]
#cnn_params = [list(sub_module.parameters()) for sub_module in cnn_subs]
#cnn_params = [item for sublist in cnn_params for item in sublist]
summary(model,
(config['input_channels'], config['input_w'], config['input_h']))
params = filter(lambda p: p.requires_grad, model.parameters())
if eff_flag == True:
params = list(params) + list(model.encoder.conv_a.parameters())
model = torch.nn.DataParallel(model)
if config['optimizer'] == 'Adam':
optimizer = optim.Adam(params,
lr=config['lr'],
weight_decay=config['weight_decay'])
elif config['optimizer'] == 'SGD':
optimizer = optim.SGD(params,
lr=config['lr'],
momentum=config['momentum'],
nesterov=config['nesterov'],
weight_decay=config['weight_decay'])
else:
raise NotImplementedError
if eff_flag == True:
cnn_params = [list(sub_module.parameters()) for sub_module in cnn_subs]
cnn_params = [item for sublist in cnn_params for item in sublist]
cnn_optimizer = torch.optim.Adam(cnn_params,
lr=0.001,
weight_decay=config['weight_decay'])
#cnn_optimizer = None
else:
cnn_optimizer = None
if config['optimizer'] == 'SGD':
if config['scheduler'] == 'CosineAnnealingLR':
scheduler = lr_scheduler.CosineAnnealingLR(
optimizer, T_max=config['epochs'], eta_min=config['min_lr'])
elif config['scheduler'] == 'ReduceLROnPlateau':
scheduler = lr_scheduler.ReduceLROnPlateau(
optimizer,
factor=config['factor'],
patience=config['patience'],
verbose=1,
min_lr=config['min_lr'])
elif config['scheduler'] == 'MultiStepLR':
scheduler = lr_scheduler.MultiStepLR(
optimizer,
milestones=[int(e) for e in config['milestones'].split(',')],
gamma=config['gamma'])
elif config['scheduler'] == 'ConstantLR':
scheduler = None
else:
raise NotImplementedError
else:
scheduler = None
# Data loading code
img_ids = glob(
os.path.join(input_folder, config['dataset'], 'images', 'training',
'*' + config['img_ext']))
train_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
#img_dir = os.path.join(input_folder, config['dataset'], 'images', 'training')
#mask_dir = os.path.join(input_folder, config['dataset'], 'annotations', 'training')
#train_image_mask = image_to_afile(img_dir, mask_dir, None, train_img_ids, config)
img_ids = glob(
os.path.join(input_folder, config['val_dataset'], 'images',
'validation', '*' + config['img_ext']))
val_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
img_ids = glob(
os.path.join(input_folder, config['val_dataset'], 'images', 'test',
'*' + config['img_ext']))
test_img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
mean = [0.485, 0.456, 0.406]
std = [0.229, 0.224, 0.225]
train_transform = Compose([
#transforms.RandomScale ([config['scale_min'], config['scale_max']]),
#transforms.RandomRotate90(),
transforms.Rotate([config['rotate_min'], config['rotate_max']],
value=mean,
mask_value=0),
transforms.Flip(),
#transforms.HorizontalFlip (),
transforms.HueSaturationValue(hue_shift_limit=10,
sat_shift_limit=10,
val_shift_limit=10),
transforms.RandomBrightnessContrast(brightness_limit=0.10,
contrast_limit=0.10,
brightness_by_max=True),
transforms.Resize(config['input_h'], config['input_w']),
transforms.Normalize(mean=mean, std=std),
])
val_transform = Compose([
transforms.Resize(config['input_h'], config['input_w']),
transforms.Normalize(mean=mean, std=std),
])
train_dataset = Dataset(img_ids=train_img_ids,
img_dir=os.path.join(input_folder,
config['dataset'], 'images',
'training'),
mask_dir=os.path.join(input_folder,
config['dataset'],
'annotations', 'training'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=train_transform,
from_file=None)
val_dataset = Dataset(img_ids=val_img_ids,
img_dir=os.path.join(input_folder,
config['val_dataset'], 'images',
'validation'),
mask_dir=os.path.join(input_folder,
config['val_dataset'],
'annotations', 'validation'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=val_transform,
from_file=None)
test_dataset = Dataset(img_ids=test_img_ids,
img_dir=os.path.join(input_folder,
config['val_dataset'],
'images', 'test'),
mask_dir=os.path.join(input_folder,
config['val_dataset'],
'annotations', 'test'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
input_channels=config['input_channels'],
transform=val_transform,
from_file=None)
train_loader = torch.utils.data.DataLoader(
train_dataset,
batch_size=config['batch_size'],
shuffle=True,
num_workers=config['num_workers'],
drop_last=True)
val_loader = torch.utils.data.DataLoader(
val_dataset,
batch_size=1, #config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
drop_last=False)
test_loader = torch.utils.data.DataLoader(
test_dataset,
batch_size=1, #config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
drop_last=False)
log = OrderedDict([
('epoch', []),
('lr', []),
('loss', []),
('iou', []),
('dice', []),
('val_loss', []),
('val_iou', []),
('val_dice', []),
])
best_iou = 0
trigger = 0
Best_dice = 0
iou_AtBestDice = 0
for epoch in range(start_epoch, config['epochs']):
print('{:s} Epoch [{:d}/{:d}]'.format(config['arch'], epoch,
config['epochs']))
# train for one epoch
train_log = train(epoch, config, train_loader, model, criterion,
optimizer, cnn_optimizer)
if config['optimizer'] == 'SGD':
if config['scheduler'] == 'CosineAnnealingLR':
scheduler.step()
elif config['scheduler'] == 'ReduceLROnPlateau':
scheduler.step(val_log['loss'])
elif config['scheduler'] == 'MultiStepLR':
scheduler.step()
# evaluate on validation set
val_log = validate(config, val_loader, model, criterion)
test_log = validate(config, test_loader, model, criterion)
if Best_dice < test_log['dice']:
Best_dice = test_log['dice']
iou_AtBestDice = test_log['iou']
print(
'loss %.4f - iou %.4f - dice %.4f - val_loss %.4f - val_iou %.4f - val_dice %.4f - test_iou %.4f - test_dice %.4f - Best_dice %.4f - iou_AtBestDice %.4f'
% (train_log['loss'], train_log['iou'], train_log['dice'],
val_log['loss'], val_log['iou'], val_log['dice'],
test_log['iou'], test_log['dice'], Best_dice, iou_AtBestDice))
save_tensorboard(writer, train_log, val_log, test_log, epoch)
log['epoch'].append(epoch)
log['lr'].append(config['lr'])
log['loss'].append(train_log['loss'])
log['iou'].append(train_log['iou'])
log['dice'].append(train_log['dice'])
log['val_loss'].append(val_log['loss'])
log['val_iou'].append(val_log['iou'])
log['val_dice'].append(val_log['dice'])
pd.DataFrame(log).to_csv(os.path.join(model_folder,
'%s/log.csv' % config['name']),
index=False)
trigger += 1
if val_log['iou'] > best_iou:
torch.save(
model.state_dict(),
os.path.join(model_folder, '%s/model.pth' % config['name']))
best_iou = val_log['iou']
print("=> saved best model")
trigger = 0
# early stopping
if config['early_stopping'] >= 0 and trigger >= config[
'early_stopping']:
print("=> early stopping")
break
torch.cuda.empty_cache()
