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datasets.py
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datasets.py
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import cv2
import os
import random
import numpy as np
from torch.utils.data import Dataset, DataLoader
import warnings
import albumentations as A
from albumentations.pytorch import ToTensorV2
from torch.utils.data.sampler import Sampler
import itertools
warnings.filterwarnings("ignore")
class ImageDataset(Dataset):
"""
dataloader for polyp segmentation tasks
refer to https://github.com/PRIS-CV/DCRNet/blob/master/utils/dataloader.py
"""
def __init__(self, cfg, roots, mode='train', trainsize=320, scale=(0.99, 1.01)):
self.cfg = cfg
self.trainsize = trainsize
self.scale = scale
self.mode = mode
self.images = []
self.gts = []
self.dataset_lens = []
for root in roots:
if mode == 'train':
self.data_root = os.path.join(root, 'TrainDataset')
self.transform = self.get_augmentation()
elif mode == 'val':
self.data_root = os.path.join(root, 'ValidationDataset')
self.transform = A.Compose(
[A.Resize(trainsize, trainsize), ])
elif mode == 'test':
self.data_root = os.path.join(root, 'TestDataset')
self.transform = A.Compose([A.Resize(trainsize, trainsize), ])
else:
raise KeyError('MODE ERROR')
image_root = os.path.join(self.data_root, 'images')
gt_root = os.path.join(self.data_root, 'masks')
_images = sorted([os.path.join(image_root, f) for f in os.listdir(image_root) if
f.endswith('.jpg') or f.endswith('.png') or f.endswith('.tif')])
_gts = sorted([os.path.join(gt_root, f) for f in os.listdir(gt_root) if
f.endswith('.jpg') or f.endswith('.png') or f.endswith('.tif')])
self.images += _images
self.gts += _gts
self.dataset_lens.append(len(self.images))
self.filter_files()
self.size = len(self.images)
self.to_tensors = A.Compose([A.Normalize(), ToTensorV2()])
def __len__(self):
return self.size
def lens(self):
return self.dataset_lens
def __getitem__(self, index):
image = cv2.imread(self.images[index])
image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
mask_3 = cv2.imread(self.gts[index])
if self.cfg.DATA.SEG_CLASSES == 1:
mask = mask_3.sum(axis=2) // 384
else:
mask = mask_3 // 128
mask = mask.astype(np.uint8)
assert mask.max() == 1 or mask.max() == 0
data_np = self.transform(image=image, mask=mask)
data_t = self.to_tensors(image=data_np['image'], mask=data_np['mask'])
data = {'imidx': index, 'path': self.images[index], 'image': data_t['image'], 'label': data_t['mask']}
return data
def filter_files(self):
assert len(self.images) == len(self.gts)
for img_path, gt_path in zip(self.images, self.gts):
img = cv2.imread(img_path)
gt = cv2.imread(gt_path)
assert gt.max() == 255
assert gt.min() == 0
assert img.shape == gt.shape
assert img_path.split('/')[-1].split('.')[0].split('_')[0] == \
gt_path.split('/')[-1].split('.')[0].split('_')[0], (img_path, gt_path)
def get_augmentation(self):
return A.Compose([
A.Resize(self.trainsize, self.trainsize),
A.HorizontalFlip(),
A.VerticalFlip(),
A.RandomRotate90(),
])
def worker_init_fn(worker_id):
random.seed(worker_id)
def iterate_once(iterable):
return np.random.permutation(iterable)
def iterate_eternally(indices):
def infinite_shuffles():
while True:
yield np.random.permutation(indices)
return itertools.chain.from_iterable(infinite_shuffles())
def grouper(iterable, n):
"""Collect data into fixed-length chunks or blocks"""
# grouper('ABCDEFG', 3) --> ABC DEF"
args = [iter(iterable)] * n
return zip(*args)
class TwoStreamBatchSampler(Sampler):
"""Iterate two sets of indices
An 'epoch' is one iteration through the primary indices.
During the epoch, the secondary indices are iterated through
as many times as needed.
"""
def __init__(self, cfg, primary_indices, secondary_indices, batch_size, secondary_batch_size):
self.cfg = cfg
self.primary_indices = primary_indices # * self.cfg.DATA.REPEAT
self.secondary_indices = secondary_indices
self.secondary_batch_size = secondary_batch_size
self.primary_batch_size = batch_size - secondary_batch_size
# print("len: ", len(self.primary_indices), len(self.secondary_indices))
assert len(self.primary_indices) >= self.primary_batch_size > 0
assert len(self.secondary_indices) >= self.secondary_batch_size >= 0
def __iter__(self):
primary_iter = iterate_once(self.primary_indices)
secondary_iter = iterate_eternally(self.secondary_indices)
if len(self.secondary_indices) == 0 and self.secondary_batch_size == 0:
return (
primary_batch + primary_batch
for (primary_batch, primary_batch)
in zip(grouper(primary_iter, self.primary_batch_size),
grouper(primary_iter, self.primary_batch_size))
)
return (
primary_batch + secondary_batch
for (primary_batch, secondary_batch)
in zip(grouper(primary_iter, self.primary_batch_size),
grouper(secondary_iter, self.secondary_batch_size))
)
def __len__(self):
return len(self.primary_indices) // self.primary_batch_size
def get_dataset(mode, cfg, trainsize=320, scale=(0.75, 1)):
# print('===mode===>', mode)
data_root = []
if "Kvasir" in cfg.DATA.NAME:
data_root.append(os.path.join(cfg.DIRS.DATA, 'Kvasir-SEG'))
if "ISIC" in cfg.DATA.NAME:
data_root.append(os.path.join(cfg.DIRS.DATA, 'ISIC'))
if mode == 'train':
dts = ImageDataset(cfg=cfg, roots=data_root, mode='train', trainsize=trainsize, scale=scale)
batch_size = cfg.TRAIN.BATCH_SIZE
total_slices = len(dts)
# print('==> total_slices', total_slices)
labeled_slice_len = int(total_slices * cfg.DATA.LABEL)
idxs = list(range(total_slices))
fold_len = int(cfg.DATA.LABEL * total_slices)
labeled_idxs = idxs[fold_len * cfg.TRAIN.FOLD: fold_len * (cfg.TRAIN.FOLD + 1)]
unlabeled_idxs = list(set(idxs) - set(labeled_idxs))
assert len(labeled_idxs) == labeled_slice_len
# print('==> labeled indexes', labeled_idxs)
# print('==> unlabeled indexes', unlabeled_idxs)
batch_sampler = TwoStreamBatchSampler(cfg,
labeled_idxs, unlabeled_idxs, batch_size,
batch_size - cfg.TRAIN.LB_BATCH_SIZE)
dataloader = DataLoader(dts, batch_sampler=batch_sampler,
num_workers=cfg.SYSTEM.NUM_WORKERS, pin_memory=True, worker_init_fn=worker_init_fn)
elif mode == 'valid':
dts = ImageDataset(cfg=cfg, roots=data_root, mode='val', trainsize=trainsize, scale=scale)
batch_size = cfg.VAL.BATCH_SIZE
dataloader = DataLoader(dts, batch_size=batch_size,
shuffle=False, drop_last=False,
num_workers=cfg.SYSTEM.NUM_WORKERS)
elif mode == 'test':
dts = ImageDataset(cfg=cfg, roots=data_root, mode='test', trainsize=trainsize, scale=scale)
batch_size = cfg.TEST.BATCH_SIZE
dataloader = DataLoader(dts, batch_size=batch_size,
shuffle=False, drop_last=False,
num_workers=cfg.SYSTEM.NUM_WORKERS)
else:
raise KeyError(f"mode error: {mode}")
return dataloader