train_augmentations = albu.Compose(
[
albu.RandomSizedCrop(
min_max_height=(
int(0.5 * (train_parameters["height_crop_size"])),
int(2 * (train_parameters["height_crop_size"])),
),
height=train_parameters["height_crop_size"],
width=train_parameters["width_crop_size"],
w2h_ratio=1.0,
p=1,
),
albu.ShiftScaleRotate(border_mode=cv2.BORDER_CONSTANT,
rotate_limit=10,
scale_limit=0,
p=0.5,
mask_value=ignore_index),
albu.RandomBrightnessContrast(p=0.5),
albu.RandomGamma(p=0.5),
albu.ImageCompression(quality_lower=20, quality_upper=100, p=0.5),
albu.GaussNoise(p=0.5),
albu.Blur(p=0.5),
albu.CoarseDropout(p=0.5, max_height=26, max_width=16),
albu.OneOf([albu.HueSaturationValue(p=0.5),
albu.RGBShift(p=0.5)],
p=0.5),
normalization,
],
p=1,
)
albumentations.Transpose(p=0.5),
albumentations.Flip(p=0.5),
albumentations.OneOf([
albumentations.CLAHE(clip_limit=2),
albumentations.IAASharpen(),
albumentations.IAAEmboss(),
albumentations.RandomBrightness(),
albumentations.RandomContrast(),
albumentations.JpegCompression(),
albumentations.Blur(),
albumentations.GaussNoise()
],
p=0.5),
# albumentations.HueSaturationValue(p=0.5),
albumentations.ShiftScaleRotate(shift_limit=0.15,
scale_limit=0.15,
rotate_limit=45,
p=0.5),
albumentations.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]),
# albumentations.ToFloat()
])
data_transforms_test = albumentations.Compose([
albumentations.Resize(args.image_height, args.image_width),
albumentations.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]),
# albumentations.ToFloat()
])
data_transforms_tta0 = albumentations.Compose([
albumentations.Resize(args.image_height, args.image_width),
def load_data(fold: int, params: Dict[str, Any]) -> Any:
torch.multiprocessing.set_sharing_strategy('file_system')
cudnn.benchmark = True
logger.info('Options:')
logger.info(pprint.pformat(opt))
full_df = pd.read_csv(opt.TRAIN.CSV)
print('full_df', full_df.shape)
train_df, val_df = train_val_split(full_df, fold)
print('train_df', train_df.shape, 'val_df', val_df.shape)
test_df = pd.read_csv(opt.TEST.CSV)
# transform_train = transforms.Compose([
# # transforms.Resize((opt.MODEL.IMAGE_SIZE)), # smaller edge
# transforms.RandomCrop(opt.MODEL.INPUT_SIZE),
# transforms.RandomHorizontalFlip(),
# # transforms.ColorJitter(brightness=0.2, contrast=0.2),
# # transforms.RandomAffine(degrees=20, scale=(0.8, 1.2), shear=10, resample=PIL.Image.BILINEAR),
# # transforms.RandomCrop(opt.MODEL.INPUT_SIZE),
# ])
augs = []
augs.append(albu.HorizontalFlip(.5))
if int(params['vflip']):
augs.append(albu.VerticalFlip(.5))
if int(params['rotate90']):
augs.append(albu.RandomRotate90())
if params['affine'] == 'soft':
augs.append(albu.ShiftScaleRotate(shift_limit=0.075, scale_limit=0.15, rotate_limit=10, p=.75))
elif params['affine'] == 'medium':
augs.append(albu.ShiftScaleRotate(shift_limit=0.0625, scale_limit=0.2, rotate_limit=45, p=0.2))
elif params['affine'] == 'hard':
augs.append(albu.ShiftScaleRotate(shift_limit=0.0625, scale_limit=0.50, rotate_limit=45, p=.75))
if float(params['noise']) > 0.1:
augs.append(albu.OneOf([
albu.IAAAdditiveGaussianNoise(),
albu.GaussNoise(),
], p=float(params['noise'])))
if float(params['blur']) > 0.1:
augs.append(albu.OneOf([
albu.MotionBlur(p=.2),
albu.MedianBlur(blur_limit=3, p=0.1),
albu.Blur(blur_limit=3, p=0.1),
], p=float(params['blur'])))
if float(params['distortion']) > 0.1:
augs.append(albu.OneOf([
albu.OpticalDistortion(p=0.3),
albu.GridDistortion(p=.1),
albu.IAAPiecewiseAffine(p=0.3),
], p=float(params['distortion'])))
if float(params['color']) > 0.1:
augs.append(albu.OneOf([
albu.CLAHE(clip_limit=2),
albu.IAASharpen(),
albu.IAAEmboss(),
albu.RandomBrightnessContrast(),
], p=float(params['color'])))
transform_train = albu.Compose([
albu.RandomCrop(height=opt.MODEL.INPUT_SIZE, width=opt.MODEL.INPUT_SIZE),
albu.Compose(augs, p=float(params['aug_global_prob']))
])
transform_test = albu.Compose([
# transforms.CenterCrop(opt.MODEL.INPUT_SIZE),
albu.RandomCrop(height=opt.MODEL.INPUT_SIZE, width=opt.MODEL.INPUT_SIZE),
albu.HorizontalFlip(),
])
train_dataset = Dataset(train_df, path=opt.TRAIN.PATH, mode='train',
num_classes=opt.MODEL.NUM_CLASSES, resize=False,
augmentor=transform_train)
val_dataset = Dataset(val_df, path=opt.TRAIN.PATH, mode='val',
# image_size=opt.MODEL.INPUT_SIZE,
num_classes=opt.MODEL.NUM_CLASSES, resize=False,
num_tta=1, # opt.TEST.NUM_TTAS,
augmentor=transform_test)
test_dataset = Dataset(test_df, path=opt.TEST.PATH, mode='test',
# image_size=opt.MODEL.INPUT_SIZE,
num_classes=opt.MODEL.NUM_CLASSES, resize=False,
num_tta=opt.TEST.NUM_TTAS,
augmentor=transform_test)
train_loader = torch.utils.data.DataLoader(
train_dataset, batch_size=opt.TRAIN.BATCH_SIZE, shuffle=True,
num_workers=opt.TRAIN.WORKERS)
val_loader = torch.utils.data.DataLoader(
val_dataset, batch_size=opt.TRAIN.BATCH_SIZE, shuffle=False, num_workers=opt.TRAIN.WORKERS)
test_loader = torch.utils.data.DataLoader(
test_dataset, batch_size=opt.TRAIN.BATCH_SIZE, shuffle=False, num_workers=opt.TRAIN.WORKERS)
return train_loader, val_loader, test_loader
g_truth = g_truth.reset_index()
g_truth = g_truth.sort_values(by='id')
return g_prob.drop('id', 1).values, g_truth['id'].values, g_truth.drop('id', 1).values
if __name__ == '__main__':
with open('SETTINGS.json', 'r') as f:
path_dict = json.load(f)
# TTA
valid_transform_aug = albumentations.Compose([
albumentations.Flip(p=0.75),
albumentations.ShiftScaleRotate(shift_limit=0.1, scale_limit=0.1, rotate_limit=90, interpolation=cv2.INTER_LINEAR,border_mode=cv2.BORDER_REFLECT_101, p=1),
albumentations.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225), max_pixel_value=255.0, p=1.0)
])
csv_path = path_dict['KAGGLE_LABEL_TRAIN_DATA_CLEAN_PATH']
df_all = pd.read_csv(csv_path)
# load test images' name
test_csv_path = path_dict['SUBMIT_CSV_PATH']
df_test = pd.read_csv(test_csv_path)
c_test = list(set(df_test['Id'].values.tolist()))
is_aug = True
num_aug = 5
batch_size = 8
normalization = albu.Normalize(mean=mean, std=std, p=1)
train_augmentations = albu.Compose(
[
albu.RandomSizedCrop(
min_max_height=(
int(0.5 * (train_parameters["height_crop_size"])),
int(2 * (train_parameters["height_crop_size"])),
),
height=train_parameters["height_crop_size"],
width=train_parameters["width_crop_size"],
w2h_ratio=1.0,
p=1,
),
albu.ShiftScaleRotate(rotate_limit=20, scale_limit=0, p=0.5),
albu.RandomBrightnessContrast(p=0.5),
albu.RandomGamma(p=0.5),
albu.HueSaturationValue(p=0.5),
albu.HorizontalFlip(p=0.5),
normalization,
],
p=1,
)
val_augmentations = albu.Compose(
[
albu.PadIfNeeded(
min_height=1024, min_width=2048, border_mode=cv2.BORDER_CONSTANT, mask_value=ignore_index, p=1
),
normalization,
RandomHorizontalFlip(0.5),
])
tensor_transform = Compose([
ToTensor(),
Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),
])
albu_transform = A.Compose([
A.LongestMaxSize(SIZE, interpolation=cv2.INTER_AREA),
A.PadIfNeeded(SIZE, SIZE, border_mode=cv2.BORDER_CONSTANT),
A.OneOf([
A.ShiftScaleRotate(scale_limit=0.2, shift_limit=0, rotate_limit=10, border_mode=cv2.BORDER_CONSTANT),
A.ElasticTransform(sigma=10, alpha_affine=10, border_mode=cv2.BORDER_CONSTANT),
]),
A.Cutout(),
A.HorizontalFlip(),
A.Normalize()
])
valid_transform = A.Compose([
A.LongestMaxSize(SIZE, interpolation=cv2.INTER_AREA),
A.PadIfNeeded(SIZE, SIZE, border_mode=cv2.BORDER_CONSTANT),
A.Normalize()
])
args['neck'] = 'option-D'
args['head'] = 'arc_margin'
args['pretrained_weights'] = None
args['optim'] = 'sgd'
args['batch_size'] = 32
args['n_splits'] = 5
args['fold'] = 0
args['seed'] = 9999
args['device'] = 'cuda:0'
args['out_dim'] = 1049
args['n_classes'] = 1000
args['class_weights'] = 'log'
args['class_weights_norm'] = 'batch'
args['normalization'] = 'imagenet'
args['crop_size'] = 448
args['tr_aug'] = A.Compose([
A.HorizontalFlip(p=0.5),
A.ImageCompression(quality_lower=99, quality_upper=100),
A.ShiftScaleRotate(shift_limit=0.2,
scale_limit=0.2,
rotate_limit=10,
border_mode=0,
p=0.7),
A.Cutout(max_h_size=int(256 * 0.4),
max_w_size=int(256 * 0.4),
num_holes=1,
p=0.5),
])
args['val_aug'] = A.Compose([
A.ImageCompression(quality_lower=99, quality_upper=100),
])
def __init__(self, hparams: Dict):
super(AircraftClassifier, self).__init__()
self.journal = logging.getLogger(__name__)
self.hparams = hparams
self.config = from_dict(AircraftClassifierConfig, hparams)
self.random_state = RandomState(self.config.random_state_seed)
#
# Statistics
#
self.epoch_fit_metrics = None
self.epoch_samples: Dict[str, ReservoirSamplingMeter] = {}
self.epoch_predictions: Dict[str, PredictionMeter] = {}
self.training_outputs = []
#
# Model
#
self.target_classes = load_classes(self.config.classes_path)
self.num_classes = len(self.target_classes)
self.model = torch.hub.load(self.config.repo,
self.config.network,
pretrained=True,
verbose=False)
self.model.fc = nn.Linear(in_features=self.model.fc.in_features,
out_features=self.num_classes)
self.group_names, self.optimizer_params = self.adjust_model_params()
self.train_accuracy = DiceAccuracy()
self.train_loss = SoftLabelCrossEntropyLoss(
smooth_factor=self.config.kv['x_lbs'],
smooth_dist=torch.full([self.num_classes],
fill_value=1.0 / self.num_classes))
self.eval_accuracy = ExactMatchAccuracy()
self.eval_loss = CrossEntropyLoss()
#
# Transforms
#
normalize_mean = [0.485, 0.456, 0.406]
normalize_std = [0.229, 0.224, 0.225]
mean_color = tuple([int(round(c * 255)) for c in normalize_mean])
self.initial_transform = AlbumentationsTransform(
albu.Compose([
albu_ext.Rescale(scale=0.5, interpolation=cv2.INTER_AREA),
albu_ext.PadToSquare(fill=mean_color)
]))
self.train_transform_mix = albu.Compose([
albu.ShiftScaleRotate(shift_limit=0.1,
scale_limit=(-0.15, 0.15),
rotate_limit=20,
border_mode=cv2.BORDER_CONSTANT,
value=mean_color,
interpolation=cv2.INTER_AREA,
p=1.0),
albu.Resize(height=224, width=224, interpolation=cv2.INTER_AREA),
albu.HorizontalFlip(p=0.5),
albu.HueSaturationValue(hue_shift_limit=30,
sat_shift_limit=30,
val_shift_limit=30,
p=1.0)
])
self.train_transform_final = albu.Compose([
albu.MultiplicativeNoise(multiplier=(0.9, 1.1), p=1.0),
albu.CoarseDropout(max_holes=12,
max_height=12,
max_width=12,
min_holes=6,
min_height=6,
min_width=6,
fill_value=mean_color,
p=1.0)
])
self.eval_transform = albu.Compose(
[albu.Resize(height=224, width=224, interpolation=cv2.INTER_AREA)])
self.model_transform = transforms.Compose([
transforms.ToTensor(),
transforms.Normalize(mean=normalize_mean, std=normalize_std)
])
self.sample_transform = torchviz_ext.InvNormalize(mean=normalize_mean,
std=normalize_std)
#
# DataLoaders
#
self.train_root_dataset = None
self.train_orig_loader = None
self.val_loader = None
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--local_rank", type=int, default=-1, help="local_rank for distributed training on gpus")
args = parser.parse_args()
torch.cuda.set_device(args.local_rank)
device = torch.device("cuda", args.local_rank)
torch.distributed.init_process_group(backend="nccl")
args.device = device
seed = 2001
random.seed(seed)
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.backends.cudnn.deterministic = True
# prepare input
import pickle
with open('../process_input/splitall/image_list_train.pickle', 'rb') as f:
image_list_train = pickle.load(f)
with open('../process_input/splitall/image_dict.pickle', 'rb') as f:
image_dict = pickle.load(f)
with open('../lung_localization/splitall/bbox_dict_train.pickle', 'rb') as f:
bbox_dict_train = pickle.load(f)
print(len(image_list_train), len(image_dict), len(bbox_dict_train))
# hyperparameters
learning_rate = 0.0004
batch_size = 32
image_size = 576
num_epoch = 1
# build model
if args.local_rank != 0:
torch.distributed.barrier()
model = seresnext50()
if args.local_rank == 0:
torch.distributed.barrier()
model.to(args.device)
num_train_steps = int(len(image_list_train)/(batch_size*4)*num_epoch) # 4 GPUs
optimizer = optim.Adam(model.parameters(), lr=learning_rate)
scheduler = get_linear_schedule_with_warmup(optimizer, num_warmup_steps=0, num_training_steps=num_train_steps)
model, optimizer = amp.initialize(model, optimizer, opt_level="O1",verbosity=0)
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[args.local_rank], output_device=args.local_rank, find_unused_parameters=True)
criterion = nn.BCEWithLogitsLoss().to(args.device)
# training
train_transform = albumentations.Compose([
albumentations.RandomContrast(limit=0.2, p=1.0),
albumentations.ShiftScaleRotate(shift_limit=0.2, scale_limit=0.2, rotate_limit=20, border_mode=cv2.BORDER_CONSTANT, p=1.0),
albumentations.Cutout(num_holes=2, max_h_size=int(0.4*image_size), max_w_size=int(0.4*image_size), fill_value=0, always_apply=True, p=1.0),
albumentations.Normalize(mean=(0.456, 0.456, 0.456), std=(0.224, 0.224, 0.224), max_pixel_value=255.0, p=1.0)
])
# iterator for training
datagen = PEDataset(image_dict=image_dict, bbox_dict=bbox_dict_train, image_list=image_list_train, target_size=image_size, transform=train_transform)
sampler = DistributedSampler(datagen)
generator = DataLoader(dataset=datagen, sampler=sampler, batch_size=batch_size, num_workers=5, pin_memory=True)
for ep in range(num_epoch):
losses = AverageMeter()
model.train()
for j,(images,labels) in enumerate(generator):
images = images.to(args.device)
labels = labels.float().to(args.device)
logits = model(images)
loss = criterion(logits.view(-1),labels)
losses.update(loss.item(), images.size(0))
optimizer.zero_grad()
with amp.scale_loss(loss, optimizer) as scaled_loss:
scaled_loss.backward()
optimizer.step()
scheduler.step()
if args.local_rank == 0:
print('epoch: {}, train_loss: {}'.format(ep,losses.avg), flush=True)
if args.local_rank == 0:
out_dir = 'weights/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
torch.save(model.module.state_dict(), out_dir+'epoch{}'.format(ep))
def create_dataloader_train_valid_test(train_batch_size=32,
valid_batch_size=16,
test_batch_size=16):
common_transform_tensor = transforms.Compose([
transforms.Resize((224, 224)),
transforms.ToTensor(),
#transforms.Normalize(mean=[0.485, 0.456, 0.406],
# std=[0.229, 0.224, 0.225])
])
normalize_mask_transform = transforms.Compose([
transforms.Resize((224, 224)),
transforms.ToTensor(),
#transforms.Normalize(mean=[0.5],
# std=[0.5])
])
train_transform = albu.Compose([
albu.RandomBrightnessContrast(p=0.5),
albu.Blur(p=0.5),
albu.HueSaturationValue(p=0.5),
albu.ShiftScaleRotate(scale_limit=(-0.1, 0),
rotate_limit=20,
border_mode=0),
albu.RGBShift(p=0.5),
albu.CLAHE(p=0.5),
albu.RandomGamma(p=0.5)
])
train_dataset, train_sampler = load_dataset(
root_dir=
'/media/huxi/DATA/inf_master/Semester-5/Thesis/code/dataset/train/',
class_name_to_id=class_name_to_id_,
aug_transform_list=[
common_transform_tensor, train_transform, normalize_mask_transform
])
valid_dataset, valid_sampler = load_dataset(
root_dir=
'/media/huxi/DATA/inf_master/Semester-5/Thesis/code/dataset/valid/',
class_name_to_id=class_name_to_id_,
aug_transform_list=[
common_transform_tensor, None, normalize_mask_transform
])
test_dataset, test_sampler = load_dataset(
root_dir=
'/media/huxi/DATA/inf_master/Semester-5/Thesis/code/dataset/test/',
class_name_to_id=class_name_to_id_,
aug_transform_list=[
common_transform_tensor, None, normalize_mask_transform
])
train_data_loader = DataLoader(train_dataset,
batch_size=train_batch_size,
sampler=train_sampler,
num_workers=8,
pin_memory=True)
valid_data_loader = DataLoader(valid_dataset,
batch_size=valid_batch_size,
sampler=valid_sampler,
num_workers=8,
pin_memory=True)
test_data_loader = DataLoader(test_dataset,
batch_size=test_batch_size,
sampler=test_sampler,
num_workers=8,
pin_memory=True)
dataloaders = {
'train': train_data_loader,
'valid': valid_data_loader,
'test': test_data_loader,
}
return dataloaders
def main():
parser = ArgumentParser(
description="Script to do data augmentation tests with albumentations."
)
parser.add_argument("data_path", type=Path, help="Path to the dataset.")
args = parser.parse_args()
data_path: Path = args.data_path
sizes = (512, 512)
p_value = 1
# Data augmentation done on cpu.
pipeline = albumentations.Compose([
albumentations.HorizontalFlip(p=0.5),
albumentations.VerticalFlip(p=0.5),
# albumentations.RandomRotate90(p=0.2),
# albumentations.CLAHE(),
albumentations.RandomBrightnessContrast(brightness_limit=0.1,
contrast_limit=0.1,
p=p_value),
albumentations.HueSaturationValue(hue_shift_limit=10,
sat_shift_limit=15,
val_shift_limit=10,
p=p_value),
albumentations.ShiftScaleRotate(scale_limit=0.05,
rotate_limit=10,
shift_limit=0.06,
p=p_value,
border_mode=cv2.BORDER_CONSTANT,
value=0),
# albumentations.GridDistortion(p=0.5),
albumentations.Normalize(mean=(0.041, 0.129, 0.03),
std=(0.054, 0.104, 0.046),
max_pixel_value=255.0,
p=1.0),
albumentations.Resize(*sizes, interpolation=cv2.INTER_LINEAR)
])
# This assumes that the masks' paths contain either "mask" or "seg" (and that the main image does not).
exts = [".jpg", ".png", ".tiff"]
img_path_list = list([
p for p in data_path.rglob('*')
if p.suffix in exts and "seg" not in str(p) and "mask" not in str(p)
])
nb_imgs = len(img_path_list)
for i, img_path in enumerate(img_path_list, start=1):
msg = f"Processing image {img_path.name} ({i}/{nb_imgs})"
print(
msg + ' ' *
(shutil.get_terminal_size(fallback=(156, 38)).columns - len(msg)),
end='\r')
img = cv2.imread(str(img_path))
img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
transformed = pipeline(image=img)
aug_img = transformed["image"]
show_img(img, "Original image")
show_img(aug_img, "Augmented normalized image")
denormalized_img = denormalize(aug_img,
mean=(0.041, 0.129, 0.03),
std=(0.054, 0.104, 0.046))
show_img(denormalized_img, "Augmented denormalized image")
self.augmentations = A.Compose(augmentations)
def __call__(self, image):
image = self.augmentations(image=image)['image']
return image
preprocess = [
A.CenterCrop(height=137, width=IMG_WIDTH),
A.Resize(height=IMG_HEIGHT, width=IMG_WIDTH, always_apply=True),
]
augmentations = [
A.PadIfNeeded(min_height=256, min_width=256, border_mode=cv2.BORDER_CONSTANT, value=[255, 255, 255], always_apply=True),
A.imgaug.transforms.IAAAffine(shear=5, mode='constant', cval=255, always_apply=True),
A.ShiftScaleRotate(rotate_limit=5, border_mode=cv2.BORDER_CONSTANT, value=[255, 255, 255], mask_value=[255, 255, 255], always_apply=True),
A.RandomCrop(height=IMG_HEIGHT, width=IMG_WIDTH, always_apply=True),
]
train_transform = transforms.Compose([
np.uint8,
transforms.Lambda(lambda x: np.array([x, x, x]).transpose((1, 2, 0)) ),
np.uint8,
Albumentations(preprocess + augmentations),
transforms.ToTensor(),
transforms.Normalize(mean=MEAN, std=STD),
# transforms.ToPILImage(),
])
valid_transform = transforms.Compose([
np.uint8,
def get_aug(aug, min_area=0.0, min_visibility=0.0):
return albumentations.Compose(
aug,
bbox_params={
"format": "pascal_voc",
"min_area": min_area,
"min_visibility": min_visibility,
"label_fields": ["category_id"],
},
)
train_augs = [
albumentations.RandomBrightnessContrast(always_apply=True),
albumentations.ShiftScaleRotate(rotate_limit=10, always_apply=True),
albumentations.augmentations.transforms.HorizontalFlip(),
# albumentations.augmentations.transforms.RandomCrop(448, 448, p=1.0),
]
class BBoxDataset(Dataset):
def __init__(self, csv_file, size=500, type="train", aug=None, fastai_out=True):
super(BBoxDataset).__init__()
if csv_file is None:
csv_file = get_one_sample_csv()
self.df = pd.read_csv(csv_file, converters={"bbox": literal_eval})
print("Dataset has {} samples.".format((self.df.shape[0])))
if type == "train":
self.aug = get_aug(train_augs) if aug is None else get_aug(aug)
else:
for ch in range(img.shape[2]):
alpha = 1.0 + random.uniform(self.contrast_limit[0],
self.contrast_limit[1])
beta = 0.0 + random.uniform(self.brightness_limit[0],
self.brightness_limit[1])
img[..., ch] = brightness_contrast_adjust(img[..., ch], alpha,
beta)
return img
albu_tfms = A.Compose([
A.OneOf([
A.ShiftScaleRotate(shift_limit=0.05,
scale_limit=0.1,
rotate_limit=15,
border_mode=cv2.BORDER_CONSTANT,
value=0),
A.OpticalDistortion(distort_limit=0.11,
shift_limit=0.15,
border_mode=cv2.BORDER_CONSTANT,
value=0),
A.NoOp()
]),
A.OneOf([
A.RandomBrightnessContrast(brightness_limit=0.5, contrast_limit=0.4),
IndependentRandomBrightnessContrast(brightness_limit=0.25,
contrast_limit=0.24),
A.RandomGamma(gamma_limit=(50, 150)),
A.NoOp()
]),
aug_types = albu.Compose([
albu.HorizontalFlip(p=0.5),
albu.OneOf([
albu.RandomBrightnessContrast(),
albu.RandomGamma(),
], p=0.3),
albu.OneOf([
albu.ElasticTransform(
alpha=120, sigma=120 * 0.05, alpha_affine=120 * 0.03),
albu.GridDistortion(),
albu.OpticalDistortion(distort_limit=2, shift_limit=0.5),
],
p=0.3),
albu.ShiftScaleRotate(scale_limit=0.1,
rotate_limit=10,
shift_limit=0.1,
p=0.5,
border_mode=0),
])
#Péparation de la base de données
listmimg = os.listdir(brain_path)
listmMask = os.listdir(mask_path)
database = {'img': listmimg, 'mask': listmMask}
print("test", database)
df = pd.DataFrame(database)
df_train, df_val = train_test_split(df, train_size=0.75, random_state=107)
df_train.to_csv('df_train.csv.gz', compression='gzip', index=False)
# A.ImageCompression(quality_lower=0.7, p=1),
A.GaussianBlur(p=1),
],
p=0.2,
),
post_transform,
])
valid_transform_3 = valid_transform_1
test_transform_3 = test_transform_1
# crop 768 and very hard augs
train_transform_4 = A.Compose([
A.ShiftScaleRotate(scale_limit=0.2,
rotate_limit=45,
border_mode=0,
value=0,
p=0.7),
A.PadIfNeeded(768, 768, border_mode=0, value=0, p=1.),
A.RandomCrop(768, 768, p=1.),
A.Flip(p=0.75),
A.Downscale(scale_min=0.5, scale_max=0.75, p=0.05),
A.MaskDropout(max_objects=3, image_fill_value=0, mask_fill_value=0, p=0.1),
# color transforms
A.OneOf(
[
A.RandomBrightnessContrast(
brightness_limit=0.3, contrast_limit=0.3, p=1),
A.RandomGamma(gamma_limit=(70, 130), p=1),
A.ChannelShuffle(p=0.2),
from tqdm import tqdm
from vision.utils.split_data import split_data
n_images = 500
bg_dir = '/home/mathias/Downloads/Linemod_preprocessed/data/01/rgb'
bgs = [os.path.join(bg_dir, f) for f in os.listdir(bg_dir)]
mask_path = 'vision/create_fence/data/fence_mask.png'
img_dir = 'vision/create_fence/data/mask_fence/images'
mask_dir = 'vision/create_fence/data/mask_fence/labels'
transforms = A.Compose([
A.ShiftScaleRotate(p=1.0),
A.HorizontalFlip(),
A.VerticalFlip(),
A.Transpose(),
A.RandomRotate90(),
A.OpticalDistortion(),
A.GridDistortion(),
A.Blur(),
A.CLAHE(),
A.RandomGamma(p=1.0),
A.GaussNoise(p=1.0)
])
def rand_color():
color = list(np.random.choice(range(10, 30), size=3))
tfms = A.Compose([
A.HorizontalFlip(),
A.OneOf([
A.RandomContrast(),
A.RandomGamma(),
A.RandomBrightness(),
],
p=0.3),
A.OneOf([
A.ElasticTransform(
alpha=120, sigma=120 * 0.05, alpha_affine=120 * 0.03),
A.GridDistortion(),
A.OpticalDistortion(distort_limit=2, shift_limit=0.5),
],
p=0.3),
A.ShiftScaleRotate(),
A.Normalize(max_pixel_value=1.0,
mean=(0.521, 0.521, 0.521),
std=(0.304, 0.304, 0.304)),
ToTensor(),
])
params = {
"batch_size":
32,
"stages": [{
"epochs": 8,
"lr": 0.001,
"freeze_to": -1
}, {
"epochs": 8,
def get_augmentations(resize: int = 224, augmentation_intensity: Optional[str] = None) -> A.Compose:
fix_seeds(24)
crop_limits = (int(resize * 0.85), resize)
if augmentation_intensity == "slight":
p_augment = 0.15
p_scale = 0.15
p_blur = 0.05
p_dropout = 0.05
p_flip = 0.15
p_noise = 0.15
gauss_limit = 0.005
elif augmentation_intensity == "light":
p_augment = 0.25
p_scale = 0.2
p_blur = 0.1
p_dropout = 0.05
p_flip = 0.2
p_noise = 0.2
gauss_limit = 0.01
elif augmentation_intensity == "medium":
p_augment = 0.5
p_scale = 0.2
p_blur = 0.2
p_dropout = 0.1
p_flip = 0.2
p_noise = 0.2
gauss_limit = 0.015
elif augmentation_intensity == "heavy":
p_augment = 0.5
p_scale = 0.35
p_blur = 0.35
p_dropout = 0.15
p_flip = 0.35
p_noise = 0.35
gauss_limit = 0.02
elif augmentation_intensity is None:
return None
else:
raise ValueError("Improper augmentation flag: should be equal to None, light, medium, or heavraisey")
augmentation = A.Compose(
[
A.OneOf(
[A.HorizontalFlip(), A.VerticalFlip()],
p=p_flip,
),
A.OneOf(
[A.Rotate(p=1.0, limit=30), A.RandomRotate90(p=1.0)],
p=p_scale,
),
A.OneOf(
[
A.ShiftScaleRotate(p=1.0, rotate_limit=30),
A.RandomSizedCrop(
min_max_height=crop_limits,
height=resize,
width=resize,
w2h_ratio=1.0,
interpolation=cv2.INTER_CUBIC,
),
],
p=p_scale,
),
A.Blur(blur_limit=3, p=p_blur),
A.CoarseDropout(max_height=7, max_width=7, p=p_dropout),
A.GaussNoise(var_limit=(0.0, gauss_limit), p=p_noise),
],
p=p_augment,
)
return augmentation
test_df = pd.read_csv("sample_submission.csv")
bbox_df = pd.read_csv("bounding_boxes.csv")
RESIZE_H = 224
RESIZE_W = 224
data_transforms = albumentations.Compose([
albumentations.Resize(RESIZE_H, RESIZE_W),
albumentations.HorizontalFlip(),
albumentations.OneOf([
albumentations.RandomContrast(),
albumentations.RandomBrightness(),
albumentations.Blur()
]),
albumentations.ShiftScaleRotate(rotate_limit=10, scale_limit=0.15),
albumentations.JpegCompression(80),
albumentations.HueSaturationValue(),
albumentations.Normalize(),
AT.ToTensor()
])
data_transforms_test = albumentations.Compose([
albumentations.Resize(RESIZE_H, RESIZE_W),
albumentations.Normalize(),
AT.ToTensor()
])
# ## Set up
torch.backends.cudnn.deterministic = True
# the following line gives ~10% speedup
# but may lead to some stochasticity in the results
torch.backends.cudnn.benchmark = True
seed_everything(cfg.SEED)
tfms = alb.Compose([
alb.HorizontalFlip(),
alb.VerticalFlip(),
alb.RandomRotate90(),
alb.RandomBrightness(),
alb.ShiftScaleRotate(shift_limit=0.0625,
scale_limit=0.2,
rotate_limit=15,
p=0.9,
border_mode=cv2.BORDER_REFLECT),
alb.OneOf([
alb.HueSaturationValue(10, 15, 10),
alb.CLAHE(clip_limit=2),
alb.RandomBrightnessContrast(),
],
p=0.3),
],
p=0.8)
df_train = pd.read_csv(cfg.csv_path)
df_train['id'] = [x[:9] for x in df_train['id'].values]
if cfg.use_test:
pass
import albumentations as A
image_size = 512
train_transforms = A.Compose(
[ #flip horizontal, randomcrop, scaling, clahe, randombrightnesscontrast, shiftscalerotate, blur
A.ShiftScaleRotate(p=0.1),
A.HorizontalFlip(p=0.5),
#A.RandomCrop(512, 512, p=0.05),
A.CLAHE(p=0.5),
A.OneOf([
A.HueSaturationValue(hue_shift_limit=0.2,
sat_shift_limit=0.2,
val_shift_limit=0.2,
p=0.5),
A.RandomBrightnessContrast(
brightness_limit=0.2, contrast_limit=0.2, p=0.5),
],
p=0.5),
A.OneOf(
[A.MedianBlur(p=0.5), A.GaussianBlur(p=0.5)], p=0.5),
A.Normalize(p=1.0),
A.Resize(height=image_size, width=image_size, p=1)
],
bbox_params=A.BboxParams(format='pascal_voc', min_visibility=0.9))
train_transforms_only_image = A.Compose(
[ #flip horizontal, randomcrop, scaling, clahe, randombrightnesscontrast, shiftscalerotate, blur
A.ShiftScaleRotate(p=0.1),
A.HorizontalFlip(p=0.5),
#A.RandomCrop(512, 512, p=0.05),
A.CLAHE(p=0.5),
normalization = albu.Normalize(mean=mean, std=std, p=1)
train_augmentations = albu.Compose(
[
albu.RandomSizedCrop(
min_max_height=(
int(0.5 * (train_parameters["height_crop_size"])),
int(2 * (train_parameters["height_crop_size"])),
),
height=train_parameters["height_crop_size"],
width=train_parameters["width_crop_size"],
w2h_ratio=1.0,
p=1,
),
albu.ShiftScaleRotate(
rotate_limit=20, scale_limit=0, p=0.5, mask_value=ignore_index),
albu.RandomBrightnessContrast(p=0.5),
albu.RandomGamma(p=0.5),
albu.HueSaturationValue(p=0.5),
albu.HorizontalFlip(p=0.5),
normalization,
],
p=1,
)
val_augmentations = albu.Compose(
[
albu.PadIfNeeded(min_height=1024,
min_width=2048,
border_mode=cv2.BORDER_CONSTANT,
mask_value=ignore_index,
return LOGGER
EXP_ID = "exp48_densenet121_backborn_75epoch_1e-4"
LOGGER_PATH = f"logs/log_{EXP_ID}.txt"
setup_logger(out_file=LOGGER_PATH)
LOGGER.info("seed={}".format(SEED))
SIZE = 128
HEIGHT = 137
WIDTH = 236
OUT_DIR = 'models'
data_transforms_96 = albumentations.Compose([
albumentations.ShiftScaleRotate(shift_limit=0.0625,
scale_limit=0.1,
rotate_limit=(5, 15),
p=0.5),
albumentations.CenterCrop(96, 96, p=1),
albumentations.Resize(256, 256, p=1),
albumentations.Cutout(num_holes=1, max_h_size=40, max_w_size=15, p=0.1),
albumentations.OneOf([
GridMask(num_grid=1, rotate=(5, 15), p=0.15),
GridMask(num_grid=2, rotate=(5, 15), p=0.15),
],
p=0.1)
])
data_transforms_104 = albumentations.Compose([
albumentations.ShiftScaleRotate(shift_limit=0.0625,
scale_limit=0.1,
rotate_limit=(5, 15),
def prepare_net(config, model, GCNModel, _use='train'):
# img_size = (config['img_size'], config['img_size'])
def worker_init_fn(worker_id):
random.seed(config['seed'] + worker_id)
if _use == 'train':
if config['optim'] == 'Adam':
optimizer = torch.optim.Adam(model.parameters(),
config['lr'],
weight_decay=config['weight_decay'])
gcn_optimizer = torch.optim.Adam(
GCNModel.parameters(),
config['lr'],
weight_decay=config['weight_decay'])
if config['optim'] == 'RMSprop':
optimizer = torch.optim.RMSprop(
model.parameters(),
config['lr'],
weight_decay=config['weight_decay'])
gcn_optimizer = torch.optim.RMSprop(
GCNModel.parameters(),
config['lr'],
weight_decay=config['weight_decay'])
elif config['optim'] == 'SGD':
optimizer = torch.optim.SGD(model.parameters(),
config['lr'],
momentum=config['momentum'],
weight_decay=config['weight_decay'],
nesterov=config['nesterov'])
gcn_optimizer = torch.optim.SGD(
GCNModel.parameters(),
config['lr'],
momentum=config['momentum'],
weight_decay=config['weight_decay'],
nesterov=config['nesterov'])
folds = [fold for fold in range(config['n_fold'])]
train_dataset = CustomDataset(
'train',
config['DataRoot'],
config['TrainFold'],
None,
transform=albumentations.Compose([
albumentations.Resize(config['img_size'], config['img_size']),
albumentations.OneOf(
[
# albumentations.RandomGamma(gamma_limit=(60, 120), p=0.9),
albumentations.RandomBrightnessContrast(
brightness_limit=0.05, contrast_limit=0.05, p=0.9),
],
p=0.5),
albumentations.OneOf(
[
albumentations.Blur(blur_limit=4, p=1),
# albumentations.MotionBlur(blur_limit=4, p=1),
# albumentations.MedianBlur(
# blur_limit=4, p=1)
],
p=0.5),
albumentations.HorizontalFlip(p=0.5),
albumentations.ShiftScaleRotate(
shift_limit=0.01,
scale_limit=0.01,
rotate_limit=3,
interpolation=cv2.INTER_LINEAR,
border_mode=cv2.BORDER_CONSTANT,
p=0.5),
# albumentations.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225), max_pixel_value=255.0, always_apply=False, p=1.0)
]),
)
labeled_df = pd.read_csv(config['TrainFold'])
labeled_fold = [i for i in config['label_fold']]
labeled_df = labeled_df[labeled_df.fold_label.isin(labeled_fold)]
labeled_fold_name = labeled_df.image.tolist()
labeled_idxs, unlabeled_idxs = relabel_dataset(train_dataset,
labeled_fold_name)
batch_sampler = TwoStreamBatchSampler(unlabeled_idxs, labeled_idxs,
config['batchsize'],
config['label_bs'])
train_loader = torch.utils.data.DataLoader(
train_dataset,
num_workers=config['num_workers'],
batch_sampler=batch_sampler,
pin_memory=True,
worker_init_fn=worker_init_fn)
# Count different classes num in train dataset
# all_label = np.array([label for _, _, label, _, _ in train_dataset])
# class_sample_count = np.array([len(np.where(all_label == t)[0]) for t in np.unique(all_label)])
# for index in range(len(config['Data_CLASSES'])):
# print("Train class {}: Num {}".format(index, class_sample_count[index]))
valid_dataset = CustomDataset('valid',
config['DataRoot'],
config['ValidFold'],
None,
transform=albumentations.Compose([
albumentations.Resize(
config['img_size'],
config['img_size']),
]))
valid_loader = torch.utils.data.DataLoader(
valid_dataset,
batch_size=10,
shuffle=False,
num_workers=config['num_workers'],
drop_last=False,
pin_memory=True,
worker_init_fn=worker_init_fn)
# Count different classes num in valid dataset
# all_label = np.array([label for _, _, label, _, _ in valid_dataset])
# class_sample_count = np.array([len(np.where(all_label == t)[0]) for t in np.unique(all_label)])
# for index in range(len(config['Data_CLASSES'])):
# print("Valid class {}: Num {}".format(index, class_sample_count[index]))
return optimizer, gcn_optimizer, train_loader, valid_loader
elif _use == 'infer':
infer_dataset = CustomDataset('infer',
config['DataRoot'],
config['TestFold'],
None,
transform=albumentations.Compose([
albumentations.Resize(
config['img_size'],
config['img_size']),
]))
infer_loader = torch.utils.data.DataLoader(
infer_dataset,
batch_size=10,
shuffle=False,
num_workers=config['num_workers'],
drop_last=False,
pin_memory=True,
worker_init_fn=worker_init_fn)
return infer_loader
alb.OneOf([
alb.GridDistortion(num_steps=8, distort_limit=0.5, p=1.0),
alb.OpticalDistortion(
distort_limit=0.5,
shift_limit=0.5,
p=1.0,
),
alb.ElasticTransform(alpha=3, p=1.0)
],
p=0.5),
alb.RandomResizedCrop(height=int(0.8192 * width_size),
width=width_size,
scale=(0.5, 1.5),
p=0.5),
alb.ShiftScaleRotate(shift_limit=0.025,
scale_limit=0.1,
rotate_limit=20,
p=0.5),
alb.CoarseDropout(max_holes=12,
min_holes=6,
max_height=int(0.8192 * width_size / 6),
max_width=int(width_size / 6),
min_height=int(0.8192 * width_size / 20),
min_width=int(width_size / 20),
p=0.5),
alb.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225)),
ToTensorV2()
])
train_set = ImagesWithAnnotationsDataset(train_df,
annot_df,
train_image_transforms,
'../ranzcr/train',
def __init__(self,
image_paths,
labels=None,
train=True,
test=False,
aug=None,
use_onehot=False):
self.paths = image_paths
self.test = test
self.use_onehot = use_onehot
if self.test == False:
self.labels = labels
self.train = train
# self.transform = albu.Compose([albu.HorizontalFlip(p=0.5),
# albu.VerticalFlip(p=0.5),
# albu.ShiftScaleRotate(rotate_limit=25.0, p=0.7),
# albu.OneOf([albu.IAAEmboss(p=1),
# albu.IAASharpen(p=1),
# albu.Blur(p=1)], p=0.5),
# albu.IAAPiecewiseAffine(p=0.5),
# albu.Resize(545, 545, always_apply=True),
# albu.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)),
# albu.pytorch.ToTensor(),
# ])
self.transform = []
self.transform.append(albu.HorizontalFlip(p=0.5))
self.transform.append(albu.VerticalFlip(p=0.5))
if aug is not None and 'rt90' in aug:
print('=> using rotate 90.')
self.transform.append(albu.RandomRotate90(p=0.5))
self.transform.append(albu.ShiftScaleRotate(rotate_limit=25.0, p=0.7))
self.transform.append(
albu.OneOf(
[albu.IAAEmboss(p=1),
albu.IAASharpen(p=1),
albu.Blur(p=1)],
p=0.5))
self.transform.append(albu.IAAPiecewiseAffine(p=0.5))
if aug is not None and 'cj' in aug:
print('=> using color jittering.')
self.transform.append(albu.RandomBrightness(p=0.5))
self.transform.append(albu.HueSaturationValue(p=0.5))
self.transform.append(albu.Resize(545, 545, always_apply=True))
if aug is not None and 'autoaug' in aug:
print('=> using autoaug.')
self.transform.append(albuImageNetPolicy())
self.transform.append(
albu.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)))
self.transform.append(albu.pytorch.ToTensor())
self.transform = albu.Compose(self.transform)
self.usere = False
if aug is not None and 're' in aug:
self.usere = True
print('=> using random erasing.')
self.re = RandomErasing()
self.default_transform = albu.Compose([
albu.Resize(545, 545, always_apply=True),
albu.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225),
always_apply=True),
albu.pytorch.ToTensor()
]) # normalized for pretrained network
"pretrained": True,
"fp16": True,
"grayscale": False,
"DEBUG": True
}
args['tr_aug'] = A.Compose(
[
# A.Resize(512, 512),
# A.RandomCrop(448, 448, p=0.5),
# A.RandomResizedCrop(512, 512),
A.Resize(512, 512),
A.Transpose(p=0.5),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.ShiftScaleRotate(p=0.5),
# A.OneOf([
# A.MotionBlur(blur_limit=5),
# A.MedianBlur(blur_limit=5),
# #A.GaussianBlur(blur_limit=5),
# A.GaussNoise(var_limit=(5.0, 30.0))], p=0.5),
# A.Normalize(),
],
p=1.)
args['val_aug'] = A.Compose(
[
# A.Resize(512, 512),
# A.RandomCrop(448, 448, p=0.5),
# A.RandomResizedCrop(512, 512),
A.Resize(512, 512),
[A.RandomBrightness(limit=0.1, p=1),
A.RandomContrast(limit=0.1, p=1)]),
A.OneOf(
[
A.MotionBlur(blur_limit=3),
A.MedianBlur(blur_limit=3),
A.GaussianBlur(blur_limit=3),
],
p=0.5,
),
A.VerticalFlip(p=0.5),
A.HorizontalFlip(p=0.5),
A.ShiftScaleRotate(
shift_limit=0.2,
scale_limit=0.2,
rotate_limit=20,
interpolation=cv2.INTER_LINEAR,
border_mode=cv2.BORDER_REFLECT_101,
p=1,
),
A.Cutout(num_holes=6, max_h_size=64, max_w_size=64, fill_value=0, p=0.5),
A.Normalize(mean=[0.4309, 0.4968, 0.3135], std=[0.2131, 0.2179, 0.1940]),
ToTensorV2(p=1.0),
])
valid_transforms = A.Compose([
A.Resize(img_size[0], img_size[1], p=1.0),
A.Normalize(mean=[0.4309, 0.4968, 0.3135], std=[0.2131, 0.2179, 0.1940]),
ToTensorV2(p=1.0),
],
p=1.0)
args.sep_conv = bool(args.sep_conv)
# for reproduciblity
if args.resume_dir is None:
make_reproducible()
# define device
device = 'cuda' if torch.cuda.is_available() else 'cpu'
# create logdir
save_path = f'logs/{args.logdir}'
mkdir(save_path)
# define augmentation
train_transform = albu.Compose([
albu.ShiftScaleRotate(shift_limit=0.125, border_mode=0, value=0, p=1),
albu.HorizontalFlip(p=0.5),
albu.CoarseDropout(max_holes=3, max_height=8, max_width=8),
albu.Normalize((0.4914, 0.4822, 0.4465), (0.247, 0.243, 0.261))
])
val_transform = albu.Compose([
albu.Normalize((0.4914, 0.4822, 0.4465), (0.247, 0.243, 0.261))
])
# load data
x_train = joblib.load('data/x_data.jl')
y_train = joblib.load('data/y_data.jl')
x_val = joblib.load('data/x_test.jl')
y_val = joblib.load('data/y_test.jl')
train_loader = get_loader(x_train, y_train, batch_size=args.batch_size, num_workers=args.num_workers,
transforms=train_transform, shuffle=True)