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def test_transform_pipeline_serialization(seed, image, mask):
aug = A.Compose(
[
A.OneOrOther(
A.Compose(
[
A.Resize(1024, 1024),
A.RandomSizedCrop(min_max_height=(256, 1024), height=512, width=512, p=1),
A.OneOf(
[
A.RandomSizedCrop(min_max_height=(256, 512), height=384, width=384, p=0.5),
A.RandomSizedCrop(min_max_height=(256, 512), height=512, width=512, p=0.5),
]
),
]
),
A.Compose(
[
A.Resize(1024, 1024),
A.RandomSizedCrop(min_max_height=(256, 1025), height=256, width=256, p=1),
A.OneOf([A.HueSaturationValue(p=0.5), A.RGBShift(p=0.7)], p=1),
pad_factor = 64
imread_library = "cv2" # can be cv2 or jpeg4py
optimizer = RAdam(
[
{"params": model.decoder.parameters(), "lr": train_parameters["lr"]},
# decrease lr for encoder in order not to permute
# pre-trained weights with large gradients on training start
{"params": model.encoder.parameters(), "lr": train_parameters["lr"] / 100},
],
weight_decay=1e-3,
)
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(
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),
n_classes = 6
label_cols = ['epidural', 'intraparenchymal', 'intraventricular', 'subarachnoid', 'subdural', 'any']
train = pd.read_csv(os.path.join(path_data, 'train.csv.gz'))
test = pd.read_csv(os.path.join(path_data, 'test.csv.gz'))
png = glob.glob(os.path.join(dir_train_img, '*.jpg'))
png = [os.path.basename(png)[:-4] for png in png]
png = np.array(png)
train = train.set_index('Image').loc[png].reset_index()
# get fold
valdf = train[train['fold']==fold].reset_index(drop=True)
trndf = train[train['fold']!=fold].reset_index(drop=True)
# Data loaders
transform_train = Compose([
HorizontalFlip(p=0.5),
ShiftScaleRotate(shift_limit=0.1, scale_limit=0.01,
rotate_limit=30, p=0.7, border_mode = cv2.BORDER_REPLICATE),
ToTensor()
])
transform_test= Compose([
ToTensor()
])
trndataset = IntracranialDataset(trndf, path=dir_train_img, transform=transform_train, labels=True)
valdataset = IntracranialDataset(valdf, path=dir_train_img, transform=transform_test, labels=False)
tstdataset = IntracranialDataset(test, path=dir_test_img, transform=transform_test, labels=False)
num_workers = 16
def get_test_transform(image_size):
longest_size = max(image_size[0], image_size[1])
return A.Compose([
#Resize(int(config.img_height*1.5),int(config.img_weight*1.5)),
CenterCrop(config.img_height,config.img_weight),
A.LongestMaxSize(longest_size, interpolation=cv2.INTER_CUBIC),
A.PadIfNeeded(image_size[0], image_size[1],
border_mode=cv2.BORDER_CONSTANT, value=0),
A.Normalize(),
ToTensor()
])
Args:
image_size:
Returns:
"""
train_transform = [
albu.Resize(*image_size),
albu.HorizontalFlip(p=0.5),
albu.ShiftScaleRotate(scale_limit=0.3, rotate_limit=15, shift_limit=0.1, p=0.5, border_mode=0),
albu.GridDistortion(p=0.5),
albu.OpticalDistortion(p=0.5, distort_limit=0.1, shift_limit=0.2),
albu.Blur(),
albu.RandomBrightnessContrast()
]
return albu.Compose(train_transform)
img = augmented['image']
if self.labels:
labels = torch.tensor(
self.data.loc[idx, label_cols])
return {'image': img, 'labels': labels}
else:
return {'image': img}
np.random.seed(SEED)
torch.manual_seed(SEED)
torch.cuda.manual_seed(SEED)
if n_gpu > 0:
torch.cuda.manual_seed_all(SEED)
torch.backends.cudnn.deterministic = True
# Data loaders
transform_train = Compose([
ShiftScaleRotate(),
ToTensor()
])
transform_test= Compose([
ToTensor()
])
logger.info('Load Dataframes')
dir_train_img = os.path.join(path_data, 'stage_1_train_images_jpg')
dir_test_img = os.path.join(path_data, 'stage_1_test_images_jpg')
# Parameters
n_classes = 6
label_cols = ['epidural', 'intraparenchymal', 'intraventricular', 'subarachnoid', 'subdural', 'any']
def transforms_train():
return A.Compose([
A.Resize(height=307, width=950),
A.RandomSizedCrop(min_max_height=(230, 307), height=256, width=896, w2h_ratio=950 / 307),
A.HorizontalFlip(),
# A.JpegCompression(quality_lower=60, quality_upper=100),
# A.RandomGamma(),
A.Normalize(mean=(Experiment.mean, Experiment.mean, Experiment.mean), std=(Experiment.std, Experiment.std, Experiment.std)),
ChannelTranspose()
])
HueSaturationValue,
IAAAdditiveGaussianNoise, GaussNoise,
RandomBrightnessContrast,
IAASharpen, IAAEmboss
)
from models.unet import UNet
from models.discriminator import FCDiscriminator
from dataset.refuge_Vmiccai import REFUGE
from pytorch_utils import (adjust_learning_rate, adjust_learning_rate_D,
calc_mse_loss, Weighted_Jaccard_loss, dice_loss)
from models import optim_weight_ema
from arguments import get_arguments
aug_student = Compose([
OneOf([
Transpose(p=0.5),
HorizontalFlip(p=0.5),
VerticalFlip(p=0.5),
RandomRotate90(p=0.5)], p=0.2),
OneOf([
IAAAdditiveGaussianNoise(p=0.5),
GaussNoise(p=0.5),
], p=0.2),
OneOf([
CLAHE(clip_limit=2),
IAASharpen(p=0.5),
IAAEmboss(p=0.5),
RandomBrightnessContrast(p=0.5),
def strong_aug(p=1.0):
return Compose([
HorizontalFlip(),
Blur(blur_limit=3),
#GridDistortion(p=.2),
#ShiftScaleRotate(shift_limit=0.0625, scale_limit=0.3, rotate_limit=0.0, p=0.7),
# OneOf([
# GridDistortion(p=.2),
# ElasticTransform(p=.2)
# ], p=0.2),
RandomContrast(p=.5, limit=0.2),
RandomBrightness(p=.5, limit=0.2),
RandomGamma(),
#RandomSizedCrop(p=0.9, min_max_height=(65, 101), height=101, width=101),
], p=p)