diff --git a/.gitignore b/.gitignore index 435f4d5..775fd72 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ __pycache__/ checkpoints/ +wandb/ diff --git a/poetry.lock b/poetry.lock index 32d039d..a5fd360 100644 --- a/poetry.lock +++ b/poetry.lock @@ -19,6 +19,36 @@ develop = ["pytest", "imgaug (>=0.4.0)"] imgaug = ["imgaug (>=0.4.0)"] tests = ["pytest"] +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asttokens" +version = "2.0.5" +description = "Annotate AST trees with source code positions" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +six = "*" + +[package.extras] +test = ["astroid", "pytest"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "black" version = "22.3.0" @@ -49,6 +79,17 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "cffi" +version = "1.15.0" +description = "Foreign Function Interface for Python calling C code." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +pycparser = "*" + [[package]] name = "charset-normalizer" version = "2.0.12" @@ -87,6 +128,22 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "debugpy" +version = "1.6.0" +description = "An implementation of the Debug Adapter Protocol for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "dev" +optional = false +python-versions = ">=3.5" + [[package]] name = "docker-pycreds" version = "0.4.0" @@ -98,6 +155,22 @@ python-versions = "*" [package.dependencies] six = ">=1.4.0" +[[package]] +name = "entrypoints" +version = 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+++ b/src/train.py @@ -2,22 +2,28 @@ import argparse import logging from pathlib import Path +import albumentations as A import torch import torch.nn as nn import torch.nn.functional as F -import wandb +from albumentations.pytorch import ToTensorV2 from torch import optim -from torch.utils.data import DataLoader, random_split +from torch.utils.data import DataLoader from tqdm import tqdm +import wandb from evaluate import evaluate -from src.utils.dataset import BasicDataset, CarvanaDataset -from unet import UNet +from src.utils.dataset import SphereDataset from src.utils.dice import dice_loss +from unet import UNet +from utils.paste import RandomPaste -dir_img = Path("./data/imgs/") -dir_mask = Path("./data/masks/") -dir_checkpoint = Path("./checkpoints/") +CHECKPOINT_DIR = Path("./checkpoints/") +DIR_TRAIN_IMG = Path("/home/lilian/data_disk/lfainsin/train2017") +DIR_VALID_IMG = Path("/home/lilian/data_disk/lfainsin/val2017/") +# DIR_VALID_MASK = Path("/home/lilian/data_disk/lfainsin/val2017mask/") +DIR_SPHERE_IMG = Path("/home/lilian/data_disk/lfainsin/spheres/Images/") +DIR_SPHERE_MASK = Path("/home/lilian/data_disk/lfainsin/spheres/Masks/") def train_net( @@ -27,37 +33,48 @@ def train_net( batch_size: int = 1, learning_rate: float = 1e-5, save_checkpoint: bool = True, - img_scale: float = 0.5, amp: bool = False, ): - # 1. Create dataset - try: - dataset = CarvanaDataset(dir_img, dir_mask, img_scale) - except (AssertionError, RuntimeError): - dataset = BasicDataset(dir_img, dir_mask, img_scale) + # 1. Create transforms + tf_train = A.Compose( + [ + A.Flip(), + A.ColorJitter(), + RandomPaste(5, 0.2, DIR_SPHERE_IMG, DIR_SPHERE_MASK), + A.ISONoise(), + A.ToFloat(max_value=255), + A.pytorch.ToTensorV2(), + ], + ) - # 2. Split into train / validation partitions - n_val = int(len(dataset) * val_percent) - n_train = len(dataset) - n_val - train_set, val_set = random_split(dataset, [n_train, n_val], generator=torch.Generator().manual_seed(0)) + tf_valid = A.Compose( + [ + RandomPaste(5, 0.2, DIR_SPHERE_IMG, DIR_SPHERE_MASK), + A.ToFloat(max_value=255), + ToTensorV2(), + ], + ) + + # 2. Create datasets + ds_train = SphereDataset(images_dir=DIR_TRAIN_IMG, transform=tf_train) + # ds_valid = SphereDataset(images_dir=DIR_VALID_IMG, masks_dir=DIR_VALID_MASK, transform=tf_valid) + ds_valid = SphereDataset(images_dir=DIR_VALID_IMG, transform=tf_valid) # 3. Create data loaders loader_args = dict(batch_size=batch_size, num_workers=4, pin_memory=True) - train_loader = DataLoader(train_set, shuffle=True, **loader_args) - val_loader = DataLoader(val_set, shuffle=False, drop_last=True, **loader_args) + train_loader = DataLoader(ds_train, shuffle=True, **loader_args) + val_loader = DataLoader(ds_valid, shuffle=False, drop_last=True, **loader_args) # (Initialize logging) - experiment = wandb.init(project="U-Net", resume="allow", anonymous="must") - experiment.config.update( - dict( + experiment = wandb.init( + project="U-Net", + config=dict( epochs=epochs, batch_size=batch_size, learning_rate=learning_rate, - val_percent=val_percent, save_checkpoint=save_checkpoint, - img_scale=img_scale, amp=amp, - ) + ), ) logging.info( @@ -65,13 +82,12 @@ def train_net( Epochs: {epochs} Batch size: {batch_size} Learning rate: {learning_rate} - Training size: {n_train} - Validation size: {n_val} + Training size: {len(ds_train)} + Validation size: {len(ds_valid)} Checkpoints: {save_checkpoint} Device: {device.type} - Images scaling: {img_scale} Mixed Precision: {amp} - """ + """ ) # 4. Set up the optimizer, the loss, the learning rate scheduler and the loss scaling for AMP @@ -85,7 +101,8 @@ def train_net( for epoch in range(1, epochs + 1): net.train() epoch_loss = 0 - with tqdm(total=n_train, desc=f"Epoch {epoch}/{epochs}", unit="img") as pbar: + + with tqdm(total=len(ds_train), desc=f"Epoch {epoch}/{epochs}", unit="img") as pbar: for batch in train_loader: images = batch["image"] true_masks = batch["mask"] @@ -119,7 +136,7 @@ def train_net( pbar.set_postfix(**{"loss (batch)": loss.item()}) # Evaluation round - division_step = n_train // (10 * batch_size) + division_step = len(ds_train) // (10 * batch_size) if division_step > 0: if global_step % division_step == 0: histograms = {} @@ -150,8 +167,8 @@ def train_net( ) if save_checkpoint: - Path(dir_checkpoint).mkdir(parents=True, exist_ok=True) - torch.save(net.state_dict(), str(dir_checkpoint / "checkpoint_epoch{}.pth".format(epoch))) + Path(CHECKPOINT_DIR).mkdir(parents=True, exist_ok=True) + torch.save(net.state_dict(), str(CHECKPOINT_DIR / "checkpoint_epoch{}.pth".format(epoch))) logging.info(f"Checkpoint {epoch} saved!") @@ -173,7 +190,7 @@ def get_args(): dest="batch_size", metavar="B", type=int, - default=1, + default=32, help="Batch size", ) parser.add_argument( @@ -192,13 +209,6 @@ def get_args(): default=False, help="Load model from a .pth file", ) - parser.add_argument( - "--scale", - "-s", - type=float, - default=0.5, - help="Downscaling factor of the images", - ) parser.add_argument( "--amp", action="store_true", @@ -220,16 +230,16 @@ if __name__ == "__main__": args = get_args() logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s") + device = torch.device("cuda" if torch.cuda.is_available() else "cpu") logging.info(f"Using device {device}") net = UNet(n_channels=3, n_classes=args.classes) logging.info( - f""" - Network:\n - \t{net.n_channels} input channels\n - \t{net.n_classes} output channels (classes)\n + f"""Network: + \t{net.n_channels} input channels + \t{net.n_classes} output channels (classes) """ ) @@ -238,6 +248,7 @@ if __name__ == "__main__": logging.info(f"Model loaded from {args.load}") net.to(device=device) + try: train_net( net=net, @@ -245,8 +256,6 @@ if __name__ == "__main__": batch_size=args.batch_size, learning_rate=args.lr, device=device, - img_scale=args.scale, - val_percent=args.val / 100, amp=args.amp, ) except KeyboardInterrupt: diff --git a/src/unet/model.py b/src/unet/model.py index 73872c5..08d2807 100644 --- a/src/unet/model.py +++ b/src/unet/model.py @@ -20,7 +20,7 @@ class UNet(nn.Module): self.ups = nn.ModuleList() for i in range(len(features) - 1): self.ups.append( - Up(*features[-1 - i : -1 - i + 3 : -1]), + Up(*features[-1 - i : -3 - i : -1]), ) self.outc = OutConv(features[0], n_classes) diff --git a/src/utils/dataset.py b/src/utils/dataset.py index 76e3a1f..6680bd8 100644 --- a/src/utils/dataset.py +++ b/src/utils/dataset.py @@ -3,6 +3,7 @@ from os import listdir from os.path import splitext from pathlib import Path +import albumentations as A import numpy as np import torch from PIL import Image @@ -10,16 +11,15 @@ from torch.utils.data import Dataset class SphereDataset(Dataset): - def __init__(self, images_dir: str, masks_dir: str, scale: float = 1.0, mask_suffix: str = ""): + def __init__(self, images_dir: str, transform: A.Compose, masks_dir: str = None): self.images_dir = Path(images_dir) - self.masks_dir = Path(masks_dir) - assert 0 < scale <= 1, "Scale must be between 0 and 1" - self.scale = scale - self.mask_suffix = mask_suffix + self.masks_dir = Path(masks_dir) if masks_dir else None self.ids = [splitext(file)[0] for file in listdir(images_dir) if not file.startswith(".")] + if not self.ids: raise RuntimeError(f"No input file found in {images_dir}, make sure you put your images there") + logging.info(f"Creating dataset with {len(self.ids)} examples") def __len__(self): @@ -30,10 +30,7 @@ class SphereDataset(Dataset): w, h = pil_img.size newW, newH = int(scale * w), int(scale * h) - assert ( - newW > 0 and newH > 0, - "Scale is too small, resized images would have no pixel", - ) + assert newW > 0 and newH > 0, "Scale is too small, resized images would have no pixel" pil_img = pil_img.resize((newW, newH), resample=Image.NEAREST if is_mask else Image.BICUBIC) img_ndarray = np.asarray(pil_img) @@ -61,25 +58,19 @@ class SphereDataset(Dataset): def __getitem__(self, idx): name = self.ids[idx] + mask_file = list(self.masks_dir.glob(name + self.mask_suffix + ".*")) img_file = list(self.images_dir.glob(name + ".*")) - assert ( - len(img_file) == 1, - f"Either no image or multiple images found for the ID {name}: {img_file}", - ) - assert ( - len(mask_file) == 1, - f"Either no mask or multiple masks found for the ID {name}: {mask_file}", - ) + assert len(img_file) == 1, f"Either no image or multiple images found for the ID {name}: {img_file}" + assert len(mask_file) == 1, f"Either no mask or multiple masks found for the ID {name}: {mask_file}" mask = self.load(mask_file[0]) img = self.load(img_file[0]) assert ( - img.size == mask.size, - f"Image and mask {name} should be the same size, but are {img.size} and {mask.size}", - ) + img.size == mask.size + ), f"Image and mask {name} should be the same size, but are {img.size} and {mask.size}" img = self.preprocess(img, self.scale, is_mask=False) mask = self.preprocess(mask, self.scale, is_mask=True) diff --git a/src/utils/paste.py b/src/utils/paste.py new file mode 100644 index 0000000..0f87c7e --- /dev/null +++ b/src/utils/paste.py @@ -0,0 +1,126 @@ +import os +import random as rd + +import albumentations as A +import cv2 +import numpy as np +from PIL import Image + + +class RandomPaste(A.DualTransform): + """Paste an object on a background. + + Args: + TODO + + Targets: + image, mask + + Image types: + uint8 + """ + + def __init__( + self, + nb, + scale_limit, + path_paste_img_dir, + path_paste_mask_dir, + always_apply=True, + p=1.0, + ): + super().__init__(always_apply, p) + self.path_paste_img_dir = path_paste_img_dir + self.path_paste_mask_dir = path_paste_mask_dir + self.scale_limit = scale_limit + self.nb = nb + + @property + def targets_as_params(self): + return ["image"] + + def apply(self, img, positions, paste_img, paste_mask, **params): + img = img.copy() + + w, h = paste_mask.shape + mask_b = paste_mask > 0 + mask_rgb_b = np.stack([mask_b, mask_b, mask_b], axis=2) + + for (x, y) in positions: + img[x : x + w, y : y + h] = img[x : x + w, y : y + h] * ~mask_rgb_b + paste_img * mask_rgb_b + + return img + + def apply_to_mask(self, mask, positions, paste_mask, **params): + mask = mask.copy() + + w, h = paste_mask.shape + mask_b = paste_mask > 0 + + for (x, y) in positions: + mask[x : x + w, y : y + h] = mask[x : x + w, y : y + h] * ~mask_b + mask_b + + return mask + + def get_params_dependent_on_targets(self, params): + filename = rd.choice(os.listdir(self.path_paste_img_dir)) + + paste_img = np.array( + Image.open( + os.path.join( + self.path_paste_img_dir, + filename, + ) + ).convert("RGB"), + dtype=np.uint8, + ) + + paste_mask = ( + np.array( + Image.open( + os.path.join( + self.path_paste_mask_dir, + filename, + ) + ).convert("L"), + dtype=np.float32, + ) + / 255 + ) + + target_img = params["image"] + + min_scale = min( + target_img.shape[0] / paste_img.shape[0], + target_img.shape[1] / paste_img.shape[1], + ) + + rescale_rotate = A.Compose( + [ + A.Rotate(limit=360, always_apply=True, border_mode=cv2.BORDER_CONSTANT), + A.RandomScale(scale_limit=(min_scale * self.scale_limit - 1, -0.99), always_apply=True), + ], + ) + + augmentations = rescale_rotate(image=paste_img, mask=paste_mask) + paste_img = augmentations["image"] + paste_mask = augmentations["mask"] + + positions = [] + for _ in range(rd.randint(1, self.nb)): + x = rd.randint(0, target_img.shape[0] - paste_img.shape[0]) + y = rd.randint(0, target_img.shape[1] - paste_img.shape[1]) + positions.append((x, y)) + + params.update( + { + "positions": positions, + "paste_img": paste_img, + "paste_mask": paste_mask, + } + ) + + return params + + def get_transform_init_args_names(self): + return "scale_limit", "path_paste_img_dir", "path_paste_mask_dir"