def __data_pipline(self, img, ldmarks):
transform = None
if self.mode == 'train':
transform = A.Compose(
[
A.Resize(height=self.output_size[0],
width=self.output_size[1],
p=1),
A.Crop(x_min=40,
y_min=0,
x_max=self.output_size[1] - 76,
y_max=self.output_size[0],
p=1),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.ToFloat(p=1),
],
keypoint_params=A.KeypointParams(format='xy'))
elif self.mode == 'test':
transform = A.Compose(
[
A.Resize(height=self.output_size[0],
width=self.output_size[1],
p=1),
A.Crop(x_min=40,
y_min=0,
x_max=self.output_size[1] - 76,
y_max=self.output_size[0],
p=1),
A.ToFloat(p=1),
],
keypoint_params=A.KeypointParams(format='xy'))
transformed = transform(image=img, keypoints=ldmarks)
return transformed
def __init__(self, outputs=6):
super().__init__()
self.net = models.resnet34(True)
self.linear = Linear(1000, outputs)
df = pd.read_csv("/home/dipet/kaggle/prostate/input/prostate-cancer-grade-assessment/train.csv")
self.train_df, self.valid_df = train_test_split(df, test_size=0.2)
self.data_dir = "/datasets/panda/train_64_100"
self.train_transforms = A.Compose(
[
A.Compose(
[
A.OneOf([A.GaussNoise(), A.MultiplicativeNoise(elementwise=True)]),
A.RandomBrightnessContrast(0.02, 0.02),
A.HueSaturationValue(0, 10, 10),
A.Flip(),
A.RandomGridShuffle(grid=(10, 10)),
A.GridDistortion(),
A.Rotate()
],
p=0.5,
),
A.ToFloat(),
]
)
self.valid_transforms = A.Compose([A.ToFloat()])
def __data_generation(self, file_path_list_temp):
'generate data containing batch_size samples'
X = []
y = []
for filename in file_path_list_temp:
# Carga de imagen y extraccion de mascara
if filename[-4:] == ".png":
image = (plt.imread(self.dir_x + filename) * 255).astype(
np.uint8)
image_masked = plt.imread(self.dir_y + filename.strip(".png") +
"-MASK.png")
else:
image = plt.imread(self.dir_x + filename).astype(np.uint8)
image_masked = plt.imread(self.dir_y + filename.strip(".tif") +
"-MASK.tif") / 255
if image.shape[2] > 3:
image[image[:, :, 3] == 0] = [255, 255, 255, 0]
image = image[:, :, :-1]
target = np.array(self.target) / 255
mask = image_masked.copy()
mask = np.all(np.abs(mask[:, :] - target) < 1e-1,
axis=2).astype(float)
mask = np.expand_dims(mask, 2)
# Definicion del pipeline de aumentaciones
augmentations_train = alb.Compose([
alb.CLAHE(p=0.1),
alb.Blur(p=0.1),
alb.RandomBrightnessContrast(p=0.1,
brightness_limit=0.2,
contrast_limit=0.2),
alb.Rotate(p=0.1, limit=5),
alb.ToFloat(max_value=255)
])
augmentations_val = alb.Compose([alb.ToFloat(max_value=255)])
# Aumentacion
if self.train:
augmented = augmentations_train(image=image, mask=mask)
else:
augmented = augmentations_val(image=image, mask=mask)
image = augmented['image']
if self.color_space == "lab":
image = color.rgb2lab(image)
image[:, :, 0] = image[:, :, 0] / 100
image[:, :, 1] = image[:, :, 1] / 128
image[:, :, 2] = image[:, :, 2] / 128
X.append(image)
y.append(augmented['mask'])
X = np.array(X).reshape(self.batch_size, self.img_size, self.img_size,
3)
y = np.array(y).reshape(self.batch_size, self.img_size, self.img_size,
1)
return X, y
def fn():
"""Default transformations"""
transform = {
'train' : [
A.Resize(448,448),
A.ToFloat(),
ToTensorV2()
],
'val' : [
A.Resize(448,448),
A.ToFloat(),
ToTensorV2()
]
}
return transform
def get_train_augm(size=Tuple[int, int],
p=0.5):
return albu.Compose([
albu.Flip(p=p),
albu.ToFloat(255),
ToTensorV2() # albu.Lambda(image=to_tensor)
])
def get_valid_augm(size=Tuple[int, int],
p=0.5):
return albu.Compose([
albu.Resize(*size),
albu.ToFloat(255),
ToTensor() # albu.Lambda(image=to_tensor)
])
def common_aug(mode, params, mean, p=1.):
'''
:param mode: 'more', 'inference', 'inference+flip', 'basic' ,
'''
augs_list = []
assert mode in {
'more',
'inference',
'inference+flip',
'basic',
}
assert max(params.augmented_image_size,
params.padded_image_size) >= params.nn_image_size
augs_list += [
albumentations.Resize(params.augmented_image_size,
params.augmented_image_size),
]
if params.padded_image_size:
augs_list += [
albumentations.PadIfNeeded(min_height=params.padded_image_size,
min_width=params.padded_image_size,
border_mode=cv2.BORDER_REFLECT_101),
]
if mode != 'inference':
if mode == 'inference+flip':
augs_list += [
albumentations.HorizontalFlip(p=1.),
]
else:
augs_list += [
albumentations.HorizontalFlip(),
]
if mode == 'more':
augs_list += [
albumentations.RandomScale(0.1),
]
if mode in ['inference', 'inference+flip']:
augs_list += [
albumentations.CenterCrop(params.nn_image_size,
params.nn_image_size),
]
else:
augs_list += [
albumentations.RandomCrop(params.nn_image_size,
params.nn_image_size),
]
augs_list += [
albumentations.ToFloat(),
albumentations.Normalize(mean=mean[0],
std=mean[1] * params.norm_sigma_k,
max_pixel_value=1.0),
]
if mode == 'more':
augs_list += [
albumentations.Blur(),
# albumentations.Rotate(limit=5),
albumentations.RandomBrightness(),
albumentations.RandomContrast(),
]
return albumentations.Compose(augs_list, p=p)
def val_dataloader(self):
hparams = self.hparams
dataset = TransformDataset(
self.valid_dataset,
albu.Compose(
[
albu.Resize(
hparams.img_height // hparams.scale_ratio,
hparams.img_width // hparams.scale_ratio,
),
albu.ToFloat(255),
ToTensorV2(),
],
bbox_params=AIEdgeDataset.bbox_params,
),
)
if hparams.gpus > 1:
sampler = data.distributed.DistributedSampler(dataset,
shuffle=True)
else:
sampler = None
return data.DataLoader(
dataset,
batch_size=hparams.batch_size,
collate_fn=CollateFn(self.net.stride, hparams, "valid"),
num_workers=hparams.num_workers,
shuffle=(sampler is None),
sampler=sampler,
pin_memory=(hparams.gpus > 0),
)
def test_dataloader(self):
hparams = self.hparams
dataset = TransformDataset(
self.test_dataset,
albu.Compose([
albu.Resize(
hparams.img_height // hparams.scale_ratio,
hparams.img_width // hparams.scale_ratio,
),
albu.ToFloat(255),
ToTensorV2(),
], ),
)
if self.hparams.gpus > 1:
sampler = data.distributed.DistributedSampler(dataset,
shuffle=False)
else:
sampler = None
return data.DataLoader(
dataset,
batch_size=hparams.batch_size,
collate_fn=AIEdgeTestDataset.collate_fn,
num_workers=hparams.num_workers,
sampler=sampler,
pin_memory=(hparams.gpus > 0),
)
def __getitem__(self, idx):
aug = albu.Compose([
albu.Flip(p=0.3),
albu.Rotate(p=0.9),
albu.Blur(p=0.4),
albu.ToFloat(p=1.)
])
# image = self.crop_im[idx]
# segment = self.crop_mask[idx]
image = self.images[idx]
# mask = self.masks[idx]
segment = self.labels_dict[self.files_names[idx]]['segment']
segment = preprocessing.rleToMask(segment).reshape((4, 256, 1600))
# mask = np.transpose(mask, (2, 1, 0))
# if image.shape != (200, 256, 4):
# image = cv2.resize(image, dsize=(200, 256))
# mask = cv2.resize(mask, dsize=(200, 256))
# image = preprocessing.one_augment(aug, image)
segment = np.transpose(segment, (1, 2, 0))
image = ToTensor()(image).float()
segment = ToTensor()(segment).float()
# mask = ToTensor()(mask).float()
return (image, segment)
def __data_generation(self, file_path_list_temp):
'generate data containing batch_size samples'
X = []
y = []
for filename in file_path_list_temp:
image = plt.imread(self.dir_x + filename)
mask = plt.imread(self.dir_y + filename)
if np.max(image) <= 1:
image *= 255
mask *= 255
if image.shape[2] > 3:
image[image[:, :, 3] == 0] = [255, 255, 255, 0]
image = image[:, :, :-1]
image = image.astype(np.uint8)
mask = mask.astype(np.uint8)
# Augmentation pipeline
augmentations_train = alb.Compose([
alb.CLAHE(p=0.1),
alb.Blur(p=0.1),
alb.RandomBrightnessContrast(p=0.1, brightness_limit=0.2, contrast_limit=0.2),
alb.Rotate(p=0.1, limit=5),
alb.ToFloat(max_value=255)
])
augmentations_val = alb.Compose([
alb.ToFloat(max_value=255)
])
# Aumentation
if self.train:
augmented = augmentations_train(image=image, mask=mask)
else:
augmented = augmentations_val(image=image, mask=mask)
image = augmented['image']
X.append(image)
y.append(augmented['mask'])
X = np.array(X).reshape(self.batch_size, self.img_size, self.img_size, 3)
y = np.array(y).reshape(self.batch_size, self.img_size, self.img_size, 1)
return X, y
def _default_test_transforms(self) -> A.Compose:
transform_ls: List[AlbumentationsTform] = [A.ToFloat()]
if self.norm_values is not None:
transform_ls.append(
A.Normalize(mean=self.norm_values.mean,
std=self.norm_values.std))
transform_ls.append(ToTensorV2())
return A.Compose(transform_ls)
def test_mydataset():
train_transforms = A.Compose([A.ToFloat(max_value=255)])
data_dirpath = f"{DIR_PATH}/data"
dataset = Mydataset(data_dirpath, train_transforms, "train")
assert len(dataset) == 9
_, img_tensor, label_tensor = dataset[0]
img = img_tensor.numpy()
assert img.shape == (3, 28, 28)
def get_byol_transforms(width, height):
byol_transforms = A.Compose([
A.Resize(width, height),
A.ToFloat(max_value=1.0),
ToTensorV2(),
])
return get_wrapper(byol_transforms)
def __init__(self):
self.Compose = albu.Compose([
albu.PadIfNeeded(min_height=40, min_width=40, border_mode=0, value=[0,0,0], always_apply=True),
albu.Cutout(num_holes=3, max_h_size=4, max_w_size=4, p=0.5),
albu.HorizontalFlip(p=0.5),
albu.RandomCrop(height=32, width=32, always_apply=True),
albu.ToFloat(max_value=None, always_apply=True),
ToTensor(normalize={'mean': [0.5071, 0.4867, 0.4408], 'std': [0.2675, 0.2565, 0.2761]})
])
def get_test_transforms(width, height):
test_transforms = A.Compose([
A.ToFloat(max_value=1.0),
A.CenterCrop(width, height),
A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),
ToTensorV2(),
])
return get_wrapper(test_transforms)
def __data_pipline(self, img, ldmarks):
# Convert RGB to BGR
transform = None
if self.mode == 'train':
transform = A.Compose(
[
A.Resize(height=self.output_size[0],
width=self.output_size[1],
p=1), # /8--->(356, 536)
A.Crop(x_min=40,
y_min=0,
x_max=self.output_size[1] - 76,
y_max=self.output_size[0],
p=1),
# A.CLAHE(p=1),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.ToFloat(p=1), # (0 ~ 1)
# A.Normalize(max_pixel_value=1, p=1)
],
keypoint_params=A.KeypointParams(format='xy'))
elif self.mode == 'test':
# import random
# random.seed(2020)
transform = A.Compose(
[
A.Resize(height=self.output_size[0],
width=self.output_size[1],
p=1), # /8--->(356, 536)
A.Crop(x_min=40,
y_min=0,
x_max=self.output_size[1] - 76,
y_max=self.output_size[0],
p=1),
# (356, 460)
# A.CLAHE(p=1),
A.ToFloat(p=1), # (0 ~ 1)
# A.Normalize(max_pixel_value=1, p=1)
],
keypoint_params=A.KeypointParams(format='xy'))
transformed = transform(image=img, keypoints=ldmarks)
return transformed
def get_common_transforms(shape, scale_ratio, pad):
h, w = shape
ph, pw = pad
return [
albu.Resize(h // scale_ratio, w // scale_ratio),
# albu.Normalize(),
albu.ToFloat(255),
PadConstant(0, cfg.ph, 0, cfg.pw),
]
def get_train_augm(size=Tuple[int, int],
p=0.5):
return albu.Compose([
albu.Resize(*size),
albu.OneOf([albu.CLAHE(6, (4, 4), always_apply=True),
albu.Equalize(always_apply=True)], p=0.99),
albu.HorizontalFlip(p=p),
albu.VerticalFlip(p=p),
albu.ToFloat(255),
ToTensor() # albu.Lambda(image=to_tensor)
])
def __init__(
self,
ann_file: str,
img_dir: str,
stage: str = "train",
transforms=A.Compose([A.ToFloat()]),
):
super().__init__()
self.coco = coco.COCO(ann_file)
self.ids = list(sorted(self.coco.imgs.keys()))
self.img_dir = img_dir
self.stage = stage
self.transforms = transforms
def compose_transforms(transforms=None):
if transforms is None:
transforms = []
transforms.append(A.ToFloat(max_value=255.0, always_apply=True), )
transforms.append(ToTensorV2(always_apply=True))
c = A.Compose(
transforms,
bbox_params=A.BboxParams(format="pascal_voc",
label_fields=["class_labels"]),
)
return c
def get_train_transforms(width, height):
train_transforms = A.Compose([
A.RandomResizedCrop(width, height, scale=(0.1, 0.8)),
A.ColorJitter(p=0.5),
A.ToFloat(max_value=1.0),
A.ShiftScaleRotate(p=0.5),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),
A.CoarseDropout(p=0.5),
ToTensorV2(),
])
return get_wrapper(train_transforms)
def __init__(
self,
root_dir: Path,
glob_search_word: str = "*.png",
crop_size: Tuple[int, int] = (224, 224),
):
assert root_dir.is_dir(), f"{root_dir} is not a directory"
self.paths = list(map(str, root_dir.glob(glob_search_word)))
assert len(self.paths) > 0, f"Not found: {root_dir}/{glob_search_word}"
self.labels = list(ChannelOrder)
self.transforms = alb.Compose([
alb.Resize(height=crop_size[0] * 2, width=crop_size[1] * 2),
alb.RandomCrop(height=crop_size[0], width=crop_size[1]),
alb.VerticalFlip(),
alb.RandomRotate90(),
alb.ToFloat(),
ToTensorV2(),
])
def __init__(self, img_dir, mask_dir, resize=None, n_channels=3, classes=1, train=False, first_channel=True):
'Initialization'
self.img_paths = glob.glob(img_dir + '/*')
self.img_dir = img_dir
self.mask_dir = mask_dir
self.resize = resize
self.n_channels = n_channels
self.first_channel = first_channel
self.classes = classes
self.train = train
self.entries = None
self.augment = albm.Compose([
albm.GaussNoise(p=0.3),
albm.RandomBrightnessContrast(brightness_limit=0.2, contrast_limit=0.2, p=0.3),
albm.ToFloat(max_value=1)
], p=1)
def train_dataloader(self):
hparams = self.hparams
augs = []
if hparams.aug_flip:
augs.append(albu.HorizontalFlip(p=1.0))
if hparams.aug_brightness:
augs.append(albu.RandomBrightness(limit=0.2, p=1.0))
if hparams.aug_randomcrop:
aug = albu.RandomSizedBBoxSafeCrop(hparams.img_height,
hparams.img_width)
augs.append(aug)
dataset = TransformDataset(
self.train_dataset,
albu.Compose(
[
*augs,
albu.Resize(hparams.img_height // 4,
hparams.img_width // 4),
albu.ToFloat(255),
ToTensorV2(),
],
bbox_params=AIEdgeDataset.bbox_params,
),
)
if self.hparams.gpus > 1:
sampler = data.distributed.DistributedSampler(dataset,
shuffle=True)
else:
sampler = None
return data.DataLoader(
dataset,
batch_size=hparams.batch_size,
collate_fn=CollateFn(self.net.stride, hparams, "train"),
num_workers=hparams.num_workers,
shuffle=(sampler is None),
sampler=sampler,
pin_memory=(hparams.gpus > 0),
drop_last=True,
)
def main():
cfg = Config()
data_man = DataManager(cfg)
tf = A.Compose([
A.Resize(width=cfg.IMG_WIDTH * 2, height=cfg.IMG_HEIGHT * 2),
A.ToFloat(),
ToTensorV2(),
])
im_folder = ImageFolder(data_man.data, tf)
loader = DataLoader(im_folder,
batch_size=64,
num_workers=cfg.NUM_WORKERS,
pin_memory=cfg.PIN_MEMORY,
shuffle=False)
mean, std = get_mean_std(loader, cfg)
print('mean', mean)
print('std', std)
def test_mydataset_loader():
train_transforms = A.Compose([A.ToFloat(max_value=255)])
data_dirpath = f"{DIR_PATH}/data"
dataset = Mydataset(data_dirpath, train_transforms, "train")
loader = torch.utils.data.DataLoader(dataset, batch_size=2)
device = "cpu"
for _, feature, label in loader:
label = label.view(-1) # [[0], [3]] -> [0, 3]とshapeを変換する
feature_np = feature.numpy()
label_np = label.numpy()
feature, label = feature.to(device), label.to(device)
break
model_output_np = numpy.array(
[
[3, 0, 0, 0, 0, 0, 0, 0, 0, 0.01],
[3, 0, 0, 0, 0, 0, 0, 0, 0, 0.01],
]
)
model_output = torch.from_numpy(model_output_np)
criterion = nn.CrossEntropyLoss()
loss = criterion(model_output, label)
assert loss.numpy() >= 0
def get_train_transforms(input_size=256):
return A.Compose(
[
A.RandomCrop(input_size, input_size),
A.HorizontalFlip(),
A.VerticalFlip(),
A.OneOf(
[
A.HueSaturationValue(
hue_shift_limit=0.2,
sat_shift_limit=0.2,
val_shift_limit=0.2,
p=0.9,
),
A.RandomBrightnessContrast(brightness_limit=0.2, contrast_limit=0.15, p=0.9),
],
p=0.9,
),
A.ToFloat(255),
ToTensorV2(),
],
additional_targets={"image1": "image"},
)
optimizer=optimizer,
callbacks=callbacks,
loaders=loaders,
logdir=logdir,
num_epochs=num_epochs,
verbose=1,
scheduler=scheduler,
main_metric='accuracy01',
minimize_metric=False,
)
## Step 2. FT with HFlip
train_dataset.augmentations = A.Compose([
A.HorizontalFlip(p=0.5),
A.ToFloat(max_value=1),
], p=1)
optimizer = torch.optim.Adam([
{'params': model.layer1.parameters(), 'lr': LR / 10},
{'params': model.layer2.parameters(), 'lr': LR / 5},
{'params': model.layer3.parameters(), 'lr': LR / 2},
{'params': model.layer4.parameters(), 'lr': LR / 1},
], lr=LR)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, factor=0.5, cooldown=1, min_lr=1e-7)
runner.train(
model=model,
criterion=criterion,
optimizer=optimizer,
ocr_file = '%s/OCR/output.txt' % (path)
metadata_length = 35
tam_max = 3
L1_layer = Lambda(lambda tensor: K.abs(tensor[0] - tensor[1]))
train_augs = [[], [], [], [], [], []]
test_augs = [[], [], [], []]
keys = ['Set01', 'Set02', 'Set03', 'Set04', 'Set05']
seq_car = albu.Compose([
albu.IAACropAndPad(px=(0, 8)),
albu.IAAAffine(scale=(0.8, 1.2),
shear=(-8, 8),
order=[0, 1],
cval=(0),
mode='constant'),
albu.ToFloat(max_value=255)
],
p=0.7)
seq_car2 = albu.Compose([
albu.IAACropAndPad(px=(0, 8)),
albu.IAAAffine(scale=(0.8, 1.2),
shear=(-8, 8),
order=[0, 1],
cval=(0),
mode='constant'),
],
p=0.7)
seq_plate = albu.Compose(
[