def get_train_augmentations(image_size: int = 224, mean: tuple = (0, 0, 0), std: tuple = (1, 1, 1)):
return A.Compose(
[
# A.RandomBrightnessContrast(brightness_limit=32, contrast_limit=(0.5, 1.5)),
# A.HueSaturationValue(hue_shift_limit=18, sat_shift_limit=(1, 2)),
# A.CoarseDropout(20),
A.Rotate(10),
A.Resize(image_size, image_size),
# A.RandomCrop(image_size, image_size, p=0.5),
A.LongestMaxSize(image_size),
# A.Equalize(mode='cv', by_channels=True, mask=None, always_apply=False, p=0.5),
# A.Normalize(mean=mean, std=std),
MinMaxScale(),
A.HorizontalFlip(),
A.PadIfNeeded(image_size, image_size, 0),
# A.Transpose(),
ToTensor(),
]
)
def _preprocess(self, x: np.ndarray, mask: Optional[np.ndarray]):
x = albu.LongestMaxSize()(image=x)['image']
x, _ = self.normalize_fn(x, x)
if mask is None:
mask = np.ones_like(x, dtype=np.float32)
else:
mask = np.round(mask.astype('float32') / 255)
h, w, _ = x.shape
block_size = 32
min_height = (h // block_size + 1) * block_size
min_width = (w // block_size + 1) * block_size
pad_params = {'mode': 'constant',
'constant_values': 0,
'pad_width': ((0, min_height - h), (0, min_width - w), (0, 0))
}
x = np.pad(x, **pad_params)
mask = np.pad(mask, **pad_params)
return map(self._array_to_batch, (x, mask)), h, w
def get_train_transform(image_size,
augmentation=None,
preprocessing=None,
crop_black=True):
if augmentation is None:
augmentation = 'none'
artificial = augmentation.endswith('-art')
if artificial:
augmentation = augmentation.replace('-art', '')
print('Using Artifical decease sings generation')
LEVELS = {
'none': get_none_augmentations,
'light': get_light_augmentations,
'medium': get_medium_augmentations,
'hard': get_hard_augmentations,
'hard2': get_hard_augmentations_v2
}
assert augmentation in LEVELS.keys()
augmentation = LEVELS[augmentation](image_size)
longest_size = max(image_size[0], image_size[1])
return A.Compose([
CropBlackRegions(tolerance=5) if crop_black else A.NoOp(
always_apply=True),
A.LongestMaxSize(longest_size, interpolation=cv2.INTER_CUBIC),
# Fake decease generation
A.Compose([AddMicroaneurisms(), AddCottonWools()],
p=float(artificial)),
A.PadIfNeeded(image_size[0],
image_size[1],
border_mode=cv2.BORDER_CONSTANT,
value=0),
augmentation,
get_preprocessing_transform(preprocessing),
A.Normalize()
])
def valid_albumentations_tfms_pets():
""" Composes a Pipeline of Albumentations Transforms for PETS dataset at the train stage
Returns:
AlbumentationsTransform: Pipeline of Albumentations Transforms
Examples::
>>> valid_tfms = valid_albumentations_tfms_pets(train=false)
>>> valid_ds = Dataset(valid_records, valid_tfms)
[[https://albumentations.readthedocs.io/en/latest/_modules/albumentations/augmentations/transforms.html/|Albumentations Transforms ]]
"""
import albumentations as A
# ImageNet stats
imagenet_mean, imagenet_std = IMAGENET_STATS
return AlbuTransform([
A.LongestMaxSize(384),
A.Normalize(mean=imagenet_mean, std=imagenet_std)
])
def __init__(self, opt):
super(Dataset3D, self).__init__()
self.opt = opt
self.augs = A.Compose([
A.LongestMaxSize(max(self.opt.input_h, self.opt.input_w), always_apply=True),
A.PadIfNeeded(self.opt.input_h, self.opt.input_w, border_mode=cv2.BORDER_CONSTANT, value=[0, 0, 0]),
A.Blur(blur_limit=(4, 8), p=0.1),
# A.ShiftScaleRotate(shift_limit=0.2, scale_limit=(-0.4, 0.2), rotate_limit=0,
# border_mode=cv2.BORDER_CONSTANT, value=(0, 0, 0), p=0.8),
A.OneOf([
A.RandomBrightnessContrast(always_apply=True),
A.RandomGamma(gamma_limit=(60, 140), always_apply=True),
# A.CLAHE(always_apply=True)
], p=0.5),
A.OneOf([
A.RGBShift(),
A.HueSaturationValue(),
A.ToGray()
], p=0.1)
],
keypoint_params=A.KeypointParams(format='xy', remove_invisible=False)
)
def transform(self):
return Compose([
albu.LongestMaxSize(np.max(
self.cfg.INSIGHTFACE.PREPROCESS.IMAGE_SIZE),
interpolation=cv2.INTER_LINEAR,
always_apply=False,
p=1),
albu.PadIfNeeded(
min_height=self.cfg.INSIGHTFACE.PREPROCESS.IMAGE_SIZE[0],
min_width=self.cfg.INSIGHTFACE.PREPROCESS.IMAGE_SIZE[1],
border_mode=cv2.BORDER_CONSTANT,
value=0,
mask_value=0,
always_apply=False,
p=1.0),
ToTensor(num_classes=1,
sigmoid=False,
normalize={
'mean': self.cfg.INSIGHTFACE.PREPROCESS.MEAN,
'std': self.cfg.INSIGHTFACE.PREPROCESS.STD
})
])
def offline_da_fn(height, width, augment=True):
da_transform = []
if augment:
da_transform += [
# A.HorizontalFlip(p=0.5),
A.ShiftScaleRotate(scale_limit=0.05, rotate_limit=7, shift_limit=0.05, border_mode=cv2.BORDER_CONSTANT,
p=1.0),
A.Perspective(scale=(0.015, 0.025), p=0.3),
A.RandomResizedCrop(height=height, width=width, scale=(0.95, 1.0), p=0.3),
# A.OneOf(
# [
# A.CLAHE(p=1),
# A.RandomBrightness(p=1),
# A.RandomGamma(p=1),
# A.RandomContrast(limit=0.1, p=1.0),
# ],
# p=0.5,
# ),
#
# A.OneOf(
# [
# A.Sharpen(alpha=(0.2, 0.5), lightness=(0.5, 1.0), p=1.0),
# A.Blur(blur_limit=[2, 3], p=1.0),
# A.GaussNoise(var_limit=(5, 25), p=1.0),
# # A.MotionBlur(blur_limit=3, p=1.0),
# ],
# p=0.5,
# ),
#
# A.Lambda(image=_da_negative, p=0.2),
]
da_transform += [
A.LongestMaxSize(max_size=max(height, width), interpolation=cv2.INTER_LANCZOS4, always_apply=True),
A.PadIfNeeded(min_height=height, min_width=width, border_mode=cv2.BORDER_CONSTANT, always_apply=True),
]
return A.Compose(da_transform)
def default_transform(self, mode="train"):
if mode == "train":
transform = A.Compose([
A.Flip(0.5),
A.ShiftScaleRotate(scale_limit=0.1, rotate_limit=45, p=0.25),
A.LongestMaxSize(max_size=800, p=1.0),
A.Normalize(mean=(0, 0, 0),
std=(1, 1, 1),
max_pixel_value=255.0,
p=1.0),
ToTensorV2(p=1.0)
],
bbox_params={
'format': 'pascal_voc',
'label_fields': ['labels']
})
elif mode == 'val':
transform = A.Compose([
A.Normalize(mean=(0, 0, 0),
std=(1, 1, 1),
max_pixel_value=255.0,
p=1.0),
ToTensorV2(p=1.0)
],
bbox_params={
'format': 'pascal_voc',
'label_fields': ['labels']
})
else:
transform = A.Compose([
A.Normalize(mean=(0, 0, 0),
std=(1, 1, 1),
max_pixel_value=255.0,
p=1.0),
ToTensorV2(p=1.0)
])
return transform
def test_fisheye_undistortion(image_fname):
image = cv2.cvtColor(cv2.imread(image_fname), cv2.COLOR_RGB2BGR)
transform = A.Compose([
CropBlackRegions(),
A.LongestMaxSize(512),
A.PadIfNeeded(512, 512, border_mode=cv2.BORDER_CONSTANT)
])
image = transform(image=image)['image']
def update(*args, **kwargs):
fx = cv2.getTrackbarPos('fx', 'Test')
k = cv2.getTrackbarPos('k', 'Test')
k_real = (k - 200) / 400
print(fx, k_real)
K = np.array([[fx, 0, 256], [0, fx, 256], [0, 0, 1]], dtype=np.float32)
# D = np.array([-2.57614020e-01, 8.77086999e-02, -2.56970803e-04, -5.93390389e-04])
D = np.array([
[k_real],
[k_real],
[0],
[0],
], dtype=np.float32)
und = removeFisheyeLensDist(image, K, D, DIM=(768, 768))
cv2.imshow('Test', und)
# cv2.waitKey(1)
cv2.namedWindow('Test')
cv2.createTrackbar('fx', 'Test', 400, 1024, update)
cv2.createTrackbar('k', 'Test', 200, 400, update)
update()
while cv2.waitKey(30) != 'q':
pass
def run(json_path, savedir, size, ignore_small=True):
data = get_data(json_path)
transform = A.Compose([A.LongestMaxSize(size)])
if not os.path.exists(savedir):
os.makedirs(savedir)
sizes = []
for info in tqdm(data):
filename = info['file_name']
identifier = os.path.basename(filename).split("_")[0]
height = info['height']
width = info['width']
image = cv2.imread(filename)
for i, a in enumerate(info['annotations']):
x, y, u, v = make_square(a['bbox'], height, width)
# TODO: maybe save segmentation? and blur background
selected_img = image[y:v, x:u].copy()
if np.min(selected_img.shape[:2]) >= size:
selected_img = transform(image=selected_img)['image']
else:
if ignore_small:
continue
#sizes.append()
sizes.append(np.min(selected_img.shape[:2]))
savepath = os.path.join(savedir, f"{identifier}_{i}.png")
# coords = []
# for points in a['segmentation']:
# xx = [k-x for k in points[::2]]
# yy = [k-y for k in points[1::2]]
# p = np.stack([xx, yy], -1).astype('int32').reshape((1, -1, 2))
# #print(p.shape)
# #print(selected_img.dtype, selected_img.shape)
# cv2.fillPoly(selected_img, p, (255, 255, 255), 8)
cv2.imwrite(savepath, selected_img)
#print(filename)
#return
print(Counter(sizes))
def __init__(self, max_size: int = 960, device: str = "cpu") -> None:
self.model = RetinaFace(
name="Resnet50",
pretrained=False,
return_layers={
"layer2": 1,
"layer3": 2,
"layer4": 3
},
in_channels=256,
out_channels=256,
).to(device)
self.device = device
self.transform = A.Compose(
[A.LongestMaxSize(max_size=max_size, p=1),
A.Normalize(p=1)])
self.max_size = max_size
self.prior_box = priorbox(
min_sizes=[[16, 32], [64, 128], [256, 512]],
steps=[8, 16, 32],
clip=False,
image_size=(self.max_size, self.max_size),
).to(device)
self.variance = [0.1, 0.2]
def get_training_albumentations():
train_transform = [
albu.LongestMaxSize(244),
albu.HorizontalFlip(),
albu.ShiftScaleRotate(scale_limit=0.5, rotate_limit=0, shift_limit=0.1, p=1, border_mode=0),
albu.PadIfNeeded(min_height=224, min_width=224, always_apply=True, border_mode=0),
albu.RandomCrop(height=224, width=224, always_apply=True),
albu.IAAAdditiveGaussianNoise(p=0.2),
albu.IAAPerspective(p=0.5),
albu.OneOf(
[
albu.CLAHE(p=1),
albu.RandomBrightness(p=1),
albu.RandomGamma(p=1),
],
p=0.9,
),
albu.OneOf(
[
albu.IAASharpen(p=1),
albu.Blur(blur_limit=3, p=1),
albu.MotionBlur(blur_limit=3, p=1),
],
p=0.9,
),
albu.OneOf(
[
albu.RandomContrast(p=1),
albu.HueSaturationValue(p=1),
],
p=0.9,
),
]
return albu.Compose(train_transform)
def resize_transforms(image_size=224):
BORDER_CONSTANT = 0
pre_size = int(image_size * 1.5)
random_crop = albu.Compose(
[
albu.SmallestMaxSize(pre_size, p=1),
albu.RandomCrop(image_size, image_size, p=1),
]
)
rescale = albu.Compose([albu.Resize(image_size, image_size, p=1)])
random_crop_big = albu.Compose(
[
albu.LongestMaxSize(pre_size, p=1),
albu.RandomCrop(image_size, image_size, p=1),
]
)
# Converts the image to a square of size image_size x image_size
result = [albu.OneOf([random_crop, rescale, random_crop_big], p=1)]
return result
def __getitem__(self, idx: int) -> Dict[str, Any]:
image_path = self.file_names[idx]
image = load_rgb(image_path)
height, width = image.shape[:2]
# Resize
resizer = albu.Compose([albu.LongestMaxSize(max_size=768, p=1)], p=1)
image = resizer(image=image)["image"]
# pad
image, pads = pad(image, factor=768)
# apply augmentations
image = self.transform(image=image)["image"]
return {
"image_id": image_path.stem,
"features": tensor_from_rgb_image(image),
"pads": np.array(pads).T,
"height": height,
"width": width,
}
def extract(json_path, datadir, savedir, size):
if not os.path.exists(savedir):
os.makedirs(savedir)
transform = A.Compose([
A.LongestMaxSize(size)
])
df = pd.read_json(json_path, lines=True)
for i, annotations in tqdm(enumerate(df['annotation'].values), total=df.shape[0]):
image_path = os.path.join(datadir, f"image_{i}.png")
image = cv2.imread(image_path)
for k, annotation in enumerate(annotations):
savepath = os.path.join(savedir, f"image_{i}_{k}.png")
height = annotation['imageHeight']
width = annotation['imageWidth']
assert image.shape[0] == height and image.shape[1] == width
if not 'Face' in annotation['label']:
print(i, annotation)
continue
points = annotation['points']
assert len(points) == 2
start, end = points
x, y = start['x'], start['y']
u, v = end['x'], end['y']
res = make_square((x, y, u, v), height, width)
x, y, u, v = res
selected_img = image[y:v, x: u]
if np.min(selected_img.shape[:2]) > size:
selected_img = transform(image=selected_img)['image']
else:
continue
cv2.imwrite(savepath, selected_img)
#print(annotation)
#break
#break
pass
def get_train_aug(RESOLUTION=300):
return A.Compose([
A.LongestMaxSize(max_size=RESOLUTION*2, interpolation=cv2.INTER_CUBIC, \
always_apply=True),
A.PadIfNeeded(min_height=RESOLUTION*2, min_width=RESOLUTION*2, always_apply=True, border_mode=cv2.BORDER_CONSTANT),
A.RandomResizedCrop(RESOLUTION,RESOLUTION, scale=(0.7, 1), \
interpolation=cv2.INTER_CUBIC),
A.Resize(RESOLUTION, RESOLUTION, p=1.0, interpolation=cv2.INTER_CUBIC),
A.FancyPCA(p=0.8, alpha=0.5),
# A.Transpose(p=0.7),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.1),
A.ShiftScaleRotate(p=0.4, rotate_limit=12),
A.HueSaturationValue(
always_apply=False, p=0.3,
hue_shift_limit=(-20, 20),
sat_shift_limit=(-30, 30),
val_shift_limit=(-20, 20)),
# A.HueSaturationValue(
# hue_shift_limit=0.4, #.3
# sat_shift_limit=0.4, #.3
# val_shift_limit=0.4, #.3
# p=0.7
# ),
A.RandomBrightnessContrast(
brightness_limit=(-0.5,0.5), #-.2,.2
contrast_limit=(-0.4, 0.4), #-.2,.2
#p=0.6
),
A.CoarseDropout(p=0.8, max_holes=30),
# A.Cutout(p=0.8, max_h_size=40, max_w_size=40),
A.Cutout(p=1, max_h_size=60, max_w_size=30, num_holes=6, fill_value=[106,87,55]),
A.Cutout(p=1, max_h_size=30, max_w_size=60, num_holes=6, fill_value=[106,87,55]),
A.OneOf([
A.OpticalDistortion(always_apply=False, p=1.0, distort_limit=(-0.6599999666213989, 0.6800000071525574),
shift_limit=(-0.6699999570846558, 0.4599999785423279), interpolation=0,
border_mode=0, value=(0, 0, 0), mask_value=None),
# A.OpticalDistortion(p=0.5, distort_limit=0.15, shift_limit=0.15),
# A.GridDistortion(p=0.5, distort_limit=0.5),
A.GridDistortion(always_apply=False, p=1.0,
num_steps=6, distort_limit=(-0.4599999785423279, 0.5),
interpolation=0, border_mode=0,
value=(0, 0, 0), mask_value=None),
# A.IAAPiecewiseAffine(p=0.5, scale=(0.1, 0.14)),
], p=0.6),
A.Sharpen(p=1.0, alpha=(0.1,0.3), lightness=(0.3, 0.9)),
A.GaussNoise(var_limit=(300.0, 500.0), p=0.4),
A.ISONoise(always_apply=False, p=0.4,
intensity=(0.10000000149011612, 1.399999976158142),
color_shift=(0.009999999776482582, 0.4000000059604645)),
A.OneOf([
A.Equalize(always_apply=False, p=1.0, mode='cv', by_channels=True),
A.Solarize(always_apply=False, p=1.0, threshold=(67, 120)),
# A.IAAAdditiveGaussianNoise(p=1.0),
A.GaussNoise(p=1.0),
A.MotionBlur(always_apply=False, p=1.0, blur_limit=(5, 20))
], p=0.5),
], p=1.0)
def get_augmentation(version):
if version == "v1":
# YOLOv2 size
size = 448
# ImageNet Normalization
normalization = A.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225), p=1)
augmentation = {
"train": A.Compose([
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.RandomRotate90(p=0.5),
A.RandomBrightnessContrast(brightness_limit=0.3, contrast_limit=0.3, p=0.25),
A.Blur(blur_limit=4, always_apply=False, p=0.25),
A.ColorJitter(brightness=0.2, contrast=0.2, saturation=0.2, hue=0.2, always_apply=False, p=0.25),
A.OneOf([
A.RandomSizedBBoxSafeCrop(size, size, erosion_rate=0.0,
interpolation=1, always_apply=False, p=0.5),
A.Resize(size, size, interpolation=1, always_apply=False, p=0.5),
], p=1),
normalization
]),
"valid": A.Compose([
A.Resize(size, size, interpolation=1, always_apply=False, p=1),
normalization
]),
}
elif version == "v2":
# YOLOv2 size
size = 448
# ImageNet Normalization
normalization = A.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225), p=1)
augmentation = {
"train": A.Compose([
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.RandomRotate90(p=0.5),
A.RandomBrightnessContrast(brightness_limit=0.3, contrast_limit=0.3, p=0.25),
A.Blur(blur_limit=4, always_apply=False, p=0.25),
A.ColorJitter(brightness=0.2, contrast=0.2, saturation=0.2, hue=0.2,
always_apply=False, p=0.25),
A.LongestMaxSize(max_size=size, interpolation=1, always_apply=False, p=1),
A.PadIfNeeded(min_height=size, min_width=size,
pad_height_divisor=None, pad_width_divisor=None,
border_mode=1, value=None, mask_value=None,
always_apply=False, p=1),
normalization
]),
"valid": A.Compose([
A.LongestMaxSize(max_size=size, interpolation=1, always_apply=False, p=1),
A.PadIfNeeded(min_height=size, min_width=size,
pad_height_divisor=None, pad_width_divisor=None,
border_mode=1, value=None, mask_value=None,
always_apply=False, p=1),
normalization
]),
}
else:
raise Exception(f"Augmentation version '{version}' is unknown!")
return augmentation
Scale = [IMAGE_SIZE // 32, IMAGE_SIZE // 16, IMAGE_SIZE // 8] # 13, 26, 52
CHECKPOINT_FILE = "checkpoint.pth.tar"
LOAD_MODEL = False
# Rescaled anchors to be between [0, 1]
# These are calculated using k-means on COCO dataset
# TODO: Recalculate for COCO
anchors = [
[(0.28, 0.22), (0.38, 0.48), (0.90, 0.78)],
[(0.07, 0.15), (0.15, 0.11), (0.14, 0.29)],
[(0.02, 0.03), (0.04, 0.07), (0.08, 0.06)]
]
train_transforms = A.Compose(
[
A.LongestMaxSize(max_size=int(IMAGE_SIZE)),
A.PadIfNeeded(min_height=int(IMAGE_SIZE), min_width=int(IMAGE_SIZE), border_mode=cv2.BORDER_CONSTANT),
A.RandomCrop(width=IMAGE_SIZE, height=IMAGE_SIZE),
A.ColorJitter(brightness=0.6, contrast=0.6, saturation=0.6, hue=0.6, p=0.1),
A.ShiftScaleRotate(rotate_limit=10, p=0.2, border_mode=cv2.BORDER_CONSTANT),
A.HorizontalFlip(p=0.5),
#A.Blur(p=0.2),
#A.CLAHE(p=0.2),
#A.Posterize(p=0.2),
A.ToGray(p=0.1),
A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225], max_pixel_value=255.0),
ToTensorV2()
],
bbox_params=A.BboxParams(format="yolo", min_visibility=0.4, label_fields=[])
)
def __init__(self, file_paths: List[Path], max_size: int,
transform: albu.Compose) -> None:
self.file_paths = file_paths
self.transform = transform
self.max_size = max_size
self.resize = albu.LongestMaxSize(max_size=max_size, p=1)
LOAD_MODEL = True
SAVE_MODEL = True
CHECKPOINT_FILE = "checkpoint.pth.tar"
IMG_DIR = DATASET + "/images/"
LABEL_DIR = DATASET + "/labels/"
ANCHORS = [
[(0.28, 0.22), (0.38, 0.48), (0.9, 0.78)],
[(0.07, 0.15), (0.15, 0.11), (0.14, 0.29)],
[(0.02, 0.03), (0.04, 0.07), (0.08, 0.06)],
] # Note these have been rescaled to be between [0, 1]
scale = 1.1
train_transforms = A.Compose(
[
A.LongestMaxSize(max_size=int(IMAGE_SIZE * scale)),
A.PadIfNeeded(
min_height=int(IMAGE_SIZE * scale),
min_width=int(IMAGE_SIZE * scale),
border_mode=cv2.BORDER_CONSTANT,
),
A.RandomCrop(width=IMAGE_SIZE, height=IMAGE_SIZE),
A.ColorJitter(
brightness=0.6, contrast=0.6, saturation=0.6, hue=0.6, p=0.4),
A.OneOf(
[
A.ShiftScaleRotate(
rotate_limit=10, p=0.4, border_mode=cv2.BORDER_CONSTANT),
A.IAAAffine(shear=10, p=0.4, mode="constant"),
],
p=1.0,
def __init__(
self,
crop_height: typing.Union[int, typing.AnyStr] = 320,
input_height: int = 224,
gaussian_blur: bool = True,
jitter_strength: float = 1.,
seed_wrap_augments: bool = False,
use_hflip_augment: bool = False,
drop_orig_image: bool = True,
crop_scale: typing.Tuple[float, float] = (0.2, 1.0),
crop_ratio: typing.Tuple[float, float] = (1.0, 1.0),
shared_transform=True,
augmentation=True, #Will be used to disable augmentation on inference / validation.
crop_strategy="centroid",
sync_hflip=False,
same_crop=False) -> None:
self.crop_height = crop_height
self.input_height = input_height
self.gaussian_blur = gaussian_blur
self.jitter_strength = jitter_strength
self.seed_wrap_augments = seed_wrap_augments
self.use_hflip_augment = use_hflip_augment
self.drop_orig_image = drop_orig_image
self.shared_transform = shared_transform
self.enable_augmentation = augmentation
self.crop_strategy = crop_strategy
self.sync_hflip = sync_hflip
self.crop_scale = crop_scale
self.crop_ratio = crop_ratio
self.same_crop = same_crop
bbox_transforms = [
albumentations.LongestMaxSize(max_size=224),
albumentations.PadIfNeeded(
min_height=224,
min_width=224,
border_mode=0,
)
]
assert self.crop_strategy in ["centroid", "bbox", "bbox_same_crop"]
if self.enable_augmentation:
augment_transforms = [
albumentations.RandomResizedCrop(
height=self.input_height,
width=self.input_height,
scale=self.crop_scale,
ratio=self.crop_ratio,
),
]
if self.crop_strategy in ["bbox", "bbox_same_crop"]:
augment_transforms = bbox_transforms + augment_transforms
if self.use_hflip_augment:
augment_transforms.append(albumentations.HorizontalFlip(p=0.5))
augment_transforms.extend([
albumentations.ColorJitter(
brightness=0.4 * self.jitter_strength,
contrast=0.4 * self.jitter_strength,
saturation=0.4 * self.jitter_strength,
hue=0.1 * self.jitter_strength,
p=0.8,
),
albumentations.ToGray(p=0.2),
])
if self.gaussian_blur:
# @@@@@ TODO: check what kernel size is best? is auto good enough?
#kernel_size = int(0.1 * self.input_height)
#if kernel_size % 2 == 0:
# kernel_size += 1
augment_transforms.append(
albumentations.GaussianBlur(
blur_limit=(3, 5),
#blur_limit=kernel_size,
#sigma_limit=???
p=0.5,
))
else:
augment_transforms = bbox_transforms
if self.seed_wrap_augments:
assert thelper_available
self.augment_transform = thelper.transforms.wrappers.SeededOpWrapper(
operation=albumentations.Compose(augment_transforms),
sample_kw="image",
)
else:
self.augment_transform = albumentations.Compose(augment_transforms)
self.convert_transform = torchvision.transforms.Compose([
torchvision.transforms.ToTensor(),
torchvision.transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
])
# add online train transform of the size of global view
self.online_augment_transform = albumentations.Compose([
albumentations.RandomResizedCrop(
height=self.input_height,
width=self.input_height,
scale=(0.5, 1.0), # @@@@ adjust if needed?
), # @@@@@@@@@ BAD W/O SEED WRAPPER?
albumentations.HorizontalFlip(
p=0.5), # @@@@@@@@@ BAD W/O SEED WRAPPER?
])
self.sync_hflip_transform = albumentations.Compose([
albumentations.HorizontalFlip(
p=1), # @@@@@@@@@ BAD W/O SEED WRAPPER?
])
def get_training_augmentation(size):
train_transform = [
A.LongestMaxSize(max_size=size, always_apply=True),
A.PadIfNeeded(min_height=size,
min_width=size,
always_apply=True,
border_mode=0),
# A.RandomCrop(height=size, width=size, always_apply=True),
# A.VerticalFlip(p=0.5),
# A.HorizontalFlip(p=0.5),
# A.RandomRotate90(p=0.5),
A.ShiftScaleRotate(scale_limit=0.2,
rotate_limit=0,
shift_limit=0.2,
p=0.1,
border_mode=0),
A.IAAPerspective(p=0.1),
A.CoarseDropout(p=0.1),
A.ChannelDropout(p=0.1),
A.RGBShift(p=0.1),
A.OneOf(
[A.OpticalDistortion(p=0.5),
A.GridDistortion(p=0.5)],
p=0.1,
),
A.OneOf(
[
A.CLAHE(p=0.5),
A.RandomBrightness(p=0.5),
A.RandomGamma(p=0.5),
],
p=0.5,
),
A.OneOf(
[
A.GaussianBlur(p=0.1),
A.IAASharpen(p=0.5),
A.Blur(blur_limit=5, p=0.5),
A.MotionBlur(blur_limit=5, p=0.5),
],
p=0.5,
),
A.OneOf(
[
A.RandomContrast(p=0.5),
A.HueSaturationValue(p=0.5),
],
p=0.1,
),
A.Lambda(mask=round_clip_0_1),
A.Cutout(num_holes=8,
max_h_size=20,
max_w_size=20,
fill_value=0,
always_apply=False,
p=0.2),
A.CoarseDropout(max_holes=8,
max_height=20,
max_width=20,
min_holes=None,
min_height=None,
min_width=None,
fill_value=0,
always_apply=False,
p=0.2),
# A.GlassBlur(sigma=0.7, max_delta=4, iterations=2, always_apply=False, mode='fast', p=0.2)
]
return A.Compose(train_transform)
'optim': 'sgd',
"batch_size": 24,
"n_splits": 5,
"fold": 0,
"seed": 0,
"device": "cuda:0",
"out_dim": 1049,
"n_classes": 1049,
'class_weights': "log",
'class_weights_norm': 'batch',
"normalization": "imagenet",
"crop_size": 448,
}
args['tr_aug'] = A.Compose([
A.LongestMaxSize(512, p=1),
A.PadIfNeeded(512, 512, border_mode=cv2.BORDER_CONSTANT, p=1),
A.RandomCrop(always_apply=False,
p=1.0,
height=args['crop_size'],
width=args['crop_size']),
A.HorizontalFlip(always_apply=False, p=0.5),
],
p=1.0)
args['val_aug'] = A.Compose([
A.LongestMaxSize(512, p=1),
A.PadIfNeeded(512, 512, border_mode=cv2.BORDER_CONSTANT, p=1),
A.CenterCrop(always_apply=False,
p=1.0,
height=args['crop_size'],
def run(datadir, n_gpus, epochs, batch_size, learning_rate):
n_max_gpus = torch.cuda.device_count()
print(f'{n_max_gpus} GPUs available')
n_gpus = min(n_gpus, n_max_gpus)
print(f'Using {n_gpus} GPUs')
device_ids = list(range(n_gpus))
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
preprocess = A.Compose([
A.LongestMaxSize(max(IMAGE_SIZE)),
A.PadIfNeeded(*IMAGE_SIZE),
A.Normalize()
])
augment = A.Compose(
[A.RandomBrightness(0.3),
A.RandomContrast(0.2),
A.HorizontalFlip()])
ds_train = StanfordDogs(datadir,
split='train',
preprocess=preprocess,
augment=augment)
ds_val = StanfordDogs(datadir, split='test', preprocess=preprocess)
n_workers = 8
dl_train = DataLoader(ds_train,
batch_size=batch_size,
shuffle=True,
num_workers=n_workers)
dl_val = DataLoader(ds_val, batch_size=batch_size, num_workers=n_workers)
model = EfficientNet(backbone='efficientnet_b2', n_classes=N_CLASSES)
model = nn.DataParallel(model, device_ids=device_ids)
model.to(device)
criterion = nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(), lr=learning_rate)
t_train_start = time.time()
for e in range(epochs):
t_epoch_start = time.time()
model.train()
for i, (images, labels) in enumerate(dl_train):
optimizer.zero_grad()
images, labels = images.to(device), labels.to(device)
logits = model(images)
loss = criterion(logits, labels)
loss.backward()
optimizer.step()
acc = accuracy(logits, labels)
epoch_time = time.time() - t_epoch_start
show_progress(e,
i,
len(dl_train),
loss=loss.detach().cpu().numpy(),
acc=acc.detach().cpu().numpy(),
epoch_time=epoch_time)
acc_val = []
model.eval()
with torch.no_grad():
for images, labels in dl_val:
images, labels = images.to(device), labels.to(device)
logits = model(images)
acc = accuracy(logits, labels)
acc_val.append(acc.cpu().numpy())
acc = np.mean(acc_val)
t_epoch = time.time() - t_epoch_start
print(f'\nEpoch{e} val-acc: {acc:.4}, time: {t_epoch:.4}s')
t_train = time.time() - t_train_start
print(f'Training finished with {t_train:.4}s')
import albumentations as A
from PIL import Image
import numpy as np
import matplotlib.pyplot as plt
import cv2
image = Image.open('image.jpg')
# print(f'PIL before convert', image.size)
image = image.convert('RGB') # needed for normalzie. W/o it there are w*h*4
# print(f'PIL after convert', image.size)
image = np.array(image)
transform = A.Compose([
# A.RandomResizedCrop(256, 256),
A.LongestMaxSize(256),
# A.SmallestMaxSize(256),
# A.Normalize(),
# A.RandomCrop(256, 256),
# A.CLAHE(), # sharpness
# A.CoarseDropout(), # rectangular
# A.ColorJitter(), # color aug
# A.Cutout(), # square
# A.Equalize(), # color aug
# A.HorizontalFlip(),
# A.HueSaturationValue(10, 10, 10, p=1) # color aug
# Pad side of the image/max if side is less than desired number
A.PadIfNeeded(256, 256, border_mode=cv2.BORDER_CONSTANT),
# A.RandomBrightness(),
# A.RandomContrast(),
# A.RandomBrightnessContrast(),
kwarg = {
'dataset': dataset,
'batch_size': batch_size,
'shuffle': shuffle,
'validation_split': validation_split,
'num_workers': num_workers,
'collate_fn': dataset.collate_fn
}
super(ChargridDataloader, self).__init__(**kwarg)
if __name__ == "__main__":
size = 64
aug = alb.Compose([
alb.LongestMaxSize(size + 24),
alb.PadIfNeeded(size + 24, size + 24, border_mode=cv2.BORDER_CONSTANT),
alb.RandomCrop(size, size, p=0.3),
alb.Resize(size, size)
], alb.BboxParams(format='coco', label_fields=['lbl_id'], min_area=2.0))
dataset = SegDataset('./data', 'train_files.txt', transform=aug)
data_loader = DataLoader(dataset,
batch_size=4,
shuffle=True,
collate_fn=dataset.collate_fn)
print(len(data_loader))
for idx, sample in enumerate(data_loader):
img, mask, boxes, lbl_boxes = sample
print(img.size())
class Yolo2(object):
width = height = 544 #
train_transform = A.Compose( # Yolo
[
# A.RandomSizedCrop(min_max_height=(800, 1024), height=1024, width=1024, p=0.5),
# A.RandomScale(scale_limit=0.3, p=1.0), # 这个有问题
C.RandomResize(scale_limit=0.3, p=1.0), # 调节长宽比 [1/1.3, 1.3]
A.OneOf(
[
A.Sequential(
[
A.SmallestMaxSize(min(height, width), p=1.0),
A.RandomCrop(height, width,
p=1.0) # 先resize到短边544，再crop成544×544
],
p=0.4),
A.LongestMaxSize(max(height, width),
p=0.6), # resize到长边544
],
p=1.0),
# A.LongestMaxSize(max(height, width), p=1.0),
A.OneOf([
A.HueSaturationValue(hue_shift_limit=0.4,
sat_shift_limit=0.4,
val_shift_limit=0.4,
p=0.9),
A.RandomBrightnessContrast(
brightness_limit=0.3, contrast_limit=0.3, p=0.9),
],
p=0.9),
# A.PadIfNeeded(min_height=height, min_width=width, border_mode=0, value=(0.5,0.5,0.5), p=1.0),
C.RandomPad(min_height=height,
min_width=width,
border_mode=0,
value=(0.5, 0.5, 0.5),
p=1.0),
A.HorizontalFlip(p=0.5),
ToTensorV2(p=1.0),
],
p=1.0,
bbox_params=A.BboxParams(format='pascal_voc',
min_area=0,
min_visibility=0,
label_fields=['labels']),
)
divisor = 32
val_transform = A.Compose( # Yolo
[
A.LongestMaxSize(width, p=1.0),
A.PadIfNeeded(min_height=height,
min_width=width,
border_mode=0,
value=(0.5, 0.5, 0.5),
p=1.0),
ToTensorV2(p=1.0),
],
p=1.0,
bbox_params=A.BboxParams(format='pascal_voc',
min_area=0,
min_visibility=0,
label_fields=['labels']))
A.IAAEmboss(),
A.RandomBrightnessContrast(),
], p=0.3),
A.Normalize(),
M.MyToTensorV2(),
],
additional_targets={
'right_img': 'image',
'left_normal': 'normal',
'right_normal': 'normal',
}
)
img_transform = A.Compose(
[
A.LongestMaxSize(max_size=IMAGE_SIZE),
A.PadIfNeeded(min_height=IMAGE_SIZE, min_width=IMAGE_SIZE, border_mode=cv2.BORDER_CONSTANT, value=0),
A.Normalize(),
M.MyToTensorV2(),
],
additional_targets={
'right_img': 'image',
}
)
_, dataloader = create_dataloader("../bdataset_stereo", "train.json", transform=my_transform)
left_imgs, right_imgs, left_normals, right_normals = next(iter(dataloader))
assert left_imgs.shape == right_imgs.shape, "dataset error"
assert right_normals.shape == left_normals.shape, "dataset error"
assert left_imgs.shape == (2, 3, 256, 256), f"dataset error {left_imgs.shape}"
assert left_normals.shape == (2, 3, 256, 256), f"dataset error {left_normals.shape}"
def pre_transforms(image_size=224):
result = [
A.LongestMaxSize(max_size=image_size),
A.PadIfNeeded(image_size, image_size, border_mode=0)
]
return result
state_dict = rename_layers(state_dict, {"model.": ""})
model.load_state_dict(state_dict)
return model
@st.cache(allow_output_mutation=True)
def cached_model():
model = load_model()
model.eval()
return model
model = cached_model()
transform = albu.Compose(
[albu.LongestMaxSize(max_size=MAX_SIZE), albu.Normalize(p=1)], p=1
)
st.title("Segment glomeruli")
# What about a TIFF image?
uploaded_file = st.file_uploader("Choose an image...", type=["jpg", "png"])
if uploaded_file is not None:
original_image = np.array(Image.open(uploaded_file))
st.image(original_image, caption="Before", use_column_width=True)
st.write("")
st.write("Detecting glomeruli...")
original_height, original_width = original_image.shape[:2]
image = transform(image=original_image)["image"]
padded_image, pads = pad(image, factor=MAX_SIZE, border=cv2.BORDER_CONSTANT)