[8eeb5a]: / data / hyperkvasir.py

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from os import listdir
from os.path import join
import PIL.Image
import matplotlib.pyplot as plt
import numpy as np
import torch.utils.data
from PIL.Image import open
from torch.nn.functional import one_hot
from torch.utils.data import Dataset
from torchvision import transforms
from perturbation.model import ModelOfNaturalVariation
import data.augmentation as aug
from utils.mask_generator import generate_a_mask
class KvasirClassificationDataset(Dataset):
"""
Dataset class that fetches images with the associated pathological class labels for use in Pretraining
"""
def __init__(self, path):
super(KvasirClassificationDataset, self).__init__()
self.path = join(path, "labeled-images/lower-gi-tract/pathological-findings")
self.label_names = listdir(self.path)
self.num_classes = len(self.label_names)
self.fname_class_dict = {}
i = 0
self.class_weights = np.zeros(self.num_classes)
for i, label in enumerate(self.label_names):
class_path = join(self.path, label)
for fname in listdir(class_path):
self.class_weights[i] += 1
self.fname_class_dict[fname] = label
self.index_dict = dict(zip(self.label_names, range(self.num_classes)))
self.common_transforms = transforms.Compose([transforms.Resize((400, 400)),
transforms.ToTensor()
])
def __len__(self):
# return 256 # for debugging
return len(self.fname_class_dict)
def __getitem__(self, item):
fname, label = list(self.fname_class_dict.items())[item]
onehot = one_hot(torch.tensor(self.index_dict[label]), num_classes=self.num_classes)
image = open(join(join(self.path, label), fname)).convert("RGB")
# print(list(image.getdata()))
# input()
image = self.common_transforms(open(join(join(self.path, label), fname)).convert("RGB"))
return image, onehot.float(), fname
class KvasirSegmentationDataset(Dataset):
"""
Dataset class that fetches images with the associated segmentation mask.
Employs "vanilla" augmentations
"""
def __init__(self, path, split="train", augment=False):
super(KvasirSegmentationDataset, self).__init__()
self.path = join(path, "segmented-images/")
self.fnames = listdir(join(self.path, "images"))
self.common_transforms = aug.pipeline_tranforms()
self.pixeltrans = aug.albumentation_pixelwise_transforms()
self.segtrans = aug.albumentation_pixelwise_transforms()
# deterministic partition
self.split = split
train_size = int(len(self.fnames) * 0.8)
val_size = (len(self.fnames) - train_size) // 2
test_size = len(self.fnames) - train_size - val_size
self.augment = augment
self.fnames_train = self.fnames[:train_size]
self.fnames_val = self.fnames[train_size:train_size + val_size]
self.fnames_test = self.fnames[train_size + val_size:]
self.split_fnames = None # iterable for selected split
if self.split == "train":
self.size = train_size
self.split_fnames = self.fnames_train
elif self.split == "val":
self.size = val_size
self.split_fnames = self.fnames_val
elif self.split == "test":
self.size = test_size
self.split_fnames = self.fnames_test
else:
raise ValueError("Choices are train/val/test")
def __len__(self):
return self.size
def __getitem__(self, index):
image = np.array(open(join(self.path, "images/", self.split_fnames[index])).convert("RGB"))
mask = np.array(open(join(self.path, "masks/", self.split_fnames[index])).convert("L"))
if self.split == "train" and self.augment == True:
transformed = self.pixeltrans(image=image)
image = transformed["image"]
segtransformed = self.segtrans(image=image, mask=mask)
image, mask = segtransformed["image"], segtransformed["mask"]
image = self.common_transforms(PIL.Image.fromarray(image))
mask = self.common_transforms(PIL.Image.fromarray(mask))
mask = (mask > 0.5).float()
return image, mask, self.split_fnames[index]
class KvasirMNVset(KvasirSegmentationDataset):
def __init__(self, path, split, inpaint=False):
super(KvasirMNVset, self).__init__(path, split, augment=False)
self.mnv = ModelOfNaturalVariation(1, use_inpainter=True)
self.p = 0.5
def __getitem__(self, index):
image = np.array(open(join(self.path, "images/", self.split_fnames[index])).convert("RGB"))
mask = np.array(open(join(self.path, "masks/", self.split_fnames[index])).convert("L"))
image = self.common_transforms(PIL.Image.fromarray(image))
mask = self.common_transforms(PIL.Image.fromarray(mask))
mask = (mask > 0.5).float()
flag = False
if self.split == "train" and np.random.rand() < self.p:
flag = True
image, mask = self.mnv(image.unsqueeze(0), mask.unsqueeze(0))
image = image.squeeze()
mask = mask.squeeze(0) # todo make this less ugly
# plt.imshow(image.T.cpu().numpy())
# plt.show()
return image, mask, self.split_fnames[index], flag
def set_prob(self, prob):
self.p = prob
class KvasirInpaintingDataset(Dataset):
def __init__(self, path, split="train"):
super(KvasirInpaintingDataset, self).__init__()
self.path = join(path, "segmented-images/")
self.fnames = listdir(join(self.path, "images"))
self.common_transforms = transforms.Compose([transforms.Resize((400, 400)),
transforms.ToTensor()
])
self.split = split
train_size = int(len(self.fnames) * 0.8)
val_size = (len(self.fnames) - train_size) // 2
test_size = len(self.fnames) - train_size - val_size
self.fnames_train = self.fnames[:train_size]
self.fnames_val = self.fnames[train_size:train_size + val_size]
self.fnames_test = self.fnames[train_size + val_size:]
self.split_fnames = None # iterable for selected split
if self.split == "train":
self.size = train_size
self.split_fnames = self.fnames_train
elif self.split == "val":
self.size = val_size
self.split_fnames = self.fnames_val
elif self.split == "test":
self.size = test_size
self.split_fnames = self.fnames_test
else:
raise ValueError("Choices are train/val/test")
def __len__(self):
return len(self.split_fnames)
def __getitem__(self, index):
image = self.common_transforms(
open(join(join(self.path, "images/"), self.split_fnames[index])).convert("RGB"))
mask = self.common_transforms(
open(join(join(self.path, "masks/"), self.split_fnames[index])).convert("L"))
mask = (mask > 0.5).float()
part = mask * image
masked_image = image - part
return image, mask, masked_image, part, self.split_fnames[index]
class KvasirSyntheticDataset(Dataset):
def __init__(self, path, split="train"):
super(KvasirSyntheticDataset, self).__init__()
self.path = join(path, "unlabeled-images")
self.fnames = listdir(join(self.path, "images"))
self.common_transforms = aug.pipeline_tranforms()
self.split = split
train_size = int(len(self.fnames) * 0.8)
val_size = (len(self.fnames) - train_size) // 2
test_size = len(self.fnames) - train_size - val_size
self.fnames_train = self.fnames[:train_size]
self.fnames_val = self.fnames[train_size:train_size + val_size]
self.fnames_test = self.fnames[train_size + val_size:]
self.split_fnames = None # iterable for selected split
if self.split == "train":
self.size = train_size
self.split_fnames = self.fnames_train
elif self.split == "val":
self.size = val_size
self.split_fnames = self.fnames_val
elif self.split == "test":
self.size = test_size
self.split_fnames = self.fnames_test
else:
raise ValueError("Choices are train/val/test")
print("loading mnv")
self.mnv = ModelOfNaturalVariation(0, use_inpainter=True).to("cuda")
print("mnv loaded")
def __len__(self):
return len(self.split_fnames)
# return 10 # debug
def __getitem__(self, index):
print(f"getting {index}")
image = np.array(open(join(self.path, "images/", self.split_fnames[index])).convert("RGB"))
mask = np.zeros_like(image)
image = self.common_transforms(PIL.Image.fromarray(image))
mask = self.common_transforms(PIL.Image.fromarray(mask))
image, mask = self.mnv(image.unsqueeze(0), mask.unsqueeze(0))
image = image.squeeze()
mask = mask.squeeze(0)
return image, mask, self.split_fnames[index]
def test_KvasirSegmentationDataset():
dataset = KvasirSegmentationDataset("Datasets/HyperKvasir", split="test")
for x, y, fname in torch.utils.data.DataLoader(dataset):
plt.imshow(x.squeeze().T)
# plt.imshow(y.squeeze().T, alpha=0.5)
plt.show()
assert isinstance(x, torch.Tensor)
assert isinstance(y, torch.Tensor)
print("Segmentation evaluation passed")
def test_KvasirClassificationDataset():
dataset = KvasirClassificationDataset("Datasets/HyperKvasir")
for x, y, fname in torch.utils.data.DataLoader(dataset):
assert isinstance(x, torch.Tensor)
assert isinstance(y, torch.Tensor)
print("Classification evaluation passed")
if __name__ == '__main__':
test_KvasirSegmentationDataset()
# test_KvasirClassificationDataset()