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dataset.py
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import torch
from torch.utils.data import Dataset
from PIL import Image, ImageChops
import pandas as pd
import os
from skimage.util import random_noise
import numpy as np
import torchvision.transforms as transforms
import json
from utils import is_image_file, pil_loader
import scipy.io as sio
class MiniImageNetDenoising(Dataset):
def __init__(self, root: str, mode: str = 'train', noise_mode='gaussian', noise_mean=0, noise_var=0.005,
noise_amount=0.05,
residual_target: bool = True, no_target: bool = False, transform=None, length=None):
"""
root (str): root path of dataset
mode (str): mode od dataset, 'train', 'val' or 'test' (default: 'train')
noise_mean (int, float): mean of Gaussian noise (default: 0)
noise_var (int, float): variance of Gaussian noise (default: 0.01)
residual_target (bool): If True, noise as target, else, the original image (default: True)
no_target (bool): If True, the output has no target, used for contrastive learning (default: False)
transform: the transform function for image (default: None)
"""
self.root = root
self.mode = mode
self.noise_mode = noise_mode
assert noise_mode in ['gaussian', 'salt', 'pepper', 's&p', 'poisson', 'gaussian+poisson']
self.mean = noise_mean
self.var = noise_var
self.amount = noise_amount
if mode not in ['train', 'val', 'test']:
raise ValueError('model can only be train, val or test')
if not os.path.exists(os.path.join(root, mode + '.csv')):
raise FileNotFoundError(os.path.join(root, mode + '.csv') + 'not found')
df = pd.read_csv(os.path.join(root, mode + '.csv'))
file_names = df['filename']
self.file_paths = [os.path.join(root, name) for name in file_names]
if length is not None:
indices = np.random.permutation(len(self.file_paths))[:length]
self.file_paths = np.array(self.file_paths)[indices]
self.residual_target = residual_target
self.transform = transform
self.no_target = no_target
self.pre_transform = None
self.post_transform = None
if transform is not None:
if not self.no_target:
self.pre_transform = []
self.post_transform = []
for t in transform.transforms:
if isinstance(t, (transforms.ToTensor, transforms.Normalize)):
self.post_transform.append(t)
else:
self.pre_transform.append(t)
self.pre_transform = transforms.Compose(self.pre_transform)
self.post_transform = transforms.Compose(self.post_transform)
elif self.no_target and isinstance(transform, list):
assert len(transform) == 2
self.pre_transform = transform[0]
self.post_transform = transform[1]
def __getitem__(self, index):
img = Image.open(self.file_paths[index])
img.convert('RGB')
if self.pre_transform is not None:
img = self.pre_transform(img)
if isinstance(self.var, (list, tuple)):
var = np.random.rand(1) * (self.var[1] - self.var[0]) + self.var[0]
else:
var = self.var
# add noise
img_np = np.array(img)
if self.mode == 'train':
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson')
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson')
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var)
else:
# fixed noise for each image, convenient for validation
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount, seed=1024 + index)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
noisy_img = Image.fromarray((255 * noisy_img).astype(np.uint8))
if self.transform is not None:
if self.no_target:
noisy_img = self.transform(noisy_img) if self.post_transform is None else self.post_transform(noisy_img)
else:
noisy_img = self.post_transform(noisy_img)
img = self.post_transform(img)
if self.no_target:
return noisy_img
else:
if self.residual_target:
target = ImageChops.subtract(noisy_img, img) if isinstance(img, Image.Image) else noisy_img - img
else:
target = img
return noisy_img, target
def __len__(self):
return len(self.file_paths)
class MiniImageNetDenoisingwithMask(MiniImageNetDenoising):
def __init__(self, root: str, mode: str = 'train', noise_mode='gaussian', noise_mean=0, noise_var=0.005,
noise_amount=0.05, residual_target: bool = True, no_target: bool = False, transform=None,
mask_generator=None, length=None):
super(MiniImageNetDenoisingwithMask, self).__init__(root, mode, noise_mode, noise_mean, noise_var,
noise_amount, residual_target, no_target, transform,
length=length)
self.mask_generator = mask_generator
def __getitem__(self, index):
img = Image.open(self.file_paths[index])
img.convert('RGB')
if self.pre_transform is not None:
img = self.pre_transform(img)
# add noise
if isinstance(self.var, (list, tuple)):
var = np.random.rand(1) * (self.var[1] - self.var[0]) + self.var[0]
else:
var = self.var
img_np = np.array(img)
if self.mode == 'train':
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson')
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson')
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var)
else:
# fixed noise for each image, convenient for validation
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount, seed=1024 + index)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
noisy_img = Image.fromarray((255 * noisy_img).astype(np.uint8))
if self.transform is not None:
if self.no_target:
noisy_img = self.transform(noisy_img) if self.post_transform is None else self.post_transform(noisy_img)
else:
noisy_img = self.post_transform(noisy_img)
img = self.post_transform(img)
if self.mask_generator is not None:
mask = self.mask_generator()
if self.no_target:
if self.mask_generator is not None:
return noisy_img, mask
return noisy_img
else:
if self.residual_target:
target = ImageChops.subtract(noisy_img, img) if isinstance(img, Image.Image) else noisy_img - img
else:
target = img
if self.mask_generator is not None:
return noisy_img, target, mask
return noisy_img, target
class NaturalNoise(Dataset):
def __init__(self, root, mode='train', transform=None, mask_generator=None):
super(NaturalNoise, self).__init__()
self.root = root
self.transform = transform
self.mask_generator = mask_generator
self.mode = mode
self.samples = []
self.targets = []
def __len__(self):
return len(self.samples)
def __getitem__(self, index):
x = Image.open(self.samples[index])
x.convert('RGB')
y = Image.open(self.targets[index])
y.convert('RGB')
if self.mode == 'train':
seed = np.random.randint(2147483647)
torch.random.manual_seed(seed)
if self.transform is not None:
x = self.transform(x)
if self.mode == 'train':
torch.random.manual_seed(seed)
y = self.transform(y)
if self.mask_generator is not None:
mask = self.mask_generator()
return x, y, mask
return x, y
class SIDD(NaturalNoise):
def __init__(self, root, mode='train', transform=None, mask_generator=None, length=None):
super(SIDD, self).__init__(root, mode, transform, mask_generator)
file_list = os.listdir(self.root)
for addr in file_list:
if os.path.isdir(os.path.join(root, addr)):
for file_name in os.listdir(os.path.join(root, addr)):
if os.path.isfile(os.path.join(root, addr, file_name)) and '.png' in file_name:
if 'NOISY' in file_name:
self.samples.append(os.path.join(root, addr, file_name))
elif 'GT' in file_name:
self.targets.append(os.path.join(root, addr, file_name))
assert len(self.samples) == len(self.targets)
if length is not None:
if mode == 'train':
self.samples = self.samples[:length]
self.targets = self.targets[:length]
else:
self.samples = self.samples[length:]
self.targets = self.targets[length:]
class FastMRI(NaturalNoise):
def __init__(self, root, mode='train', transform=None, mask_generator=None):
super(FastMRI, self).__init__(root, mode, transform, mask_generator)
file_list = os.listdir(self.root)
for addr in file_list:
if os.path.isdir(os.path.join(root, addr)):
for file_name in os.listdir(os.path.join(root, addr)):
if os.path.isfile(os.path.join(root, addr, file_name)) and '.png' in file_name:
if addr == 'noisy':
self.samples.append(os.path.join(root, addr, file_name))
elif addr == 'gt':
self.targets.append(os.path.join(root, addr, file_name))
assert len(self.samples) == len(self.targets)
class PolyU(NaturalNoise):
def __init__(self, root, mode='train', transform=None, mask_generator=None, length=None):
super(PolyU, self).__init__(root, mode, transform, mask_generator)
file_list = os.listdir(self.root)
for addr in file_list:
if addr.endswith('real.JPG') or addr.endswith('real.jpg'):
self.samples.append(os.path.join(root, addr))
addr = addr.replace('real', 'mean')
if os.path.isfile(os.path.join(root, addr)):
self.targets.append(os.path.join(root, addr))
else:
raise FileNotFoundError('The corresponding clean image of {} does\'t exist.'.format(addr))
if length is not None:
if mode == 'train':
self.samples = self.samples[:30] + self.samples[-30:]
self.targets = self.targets[:30] + self.targets[-30:]
else:
self.samples = self.samples[30:-30]
self.targets = self.targets[30:-30]
class SimulatedNoise(Dataset):
def __init__(self, root, mode='train', transform=None, mask_generator=None, residual_target=True,
noise_mode='gaussian', noise_mean=0, noise_var=0.005, noise_amount=0.05, channel=3, train_test=None):
super(SimulatedNoise, self).__init__()
self.root = root
self.transform = transform
self.mask_generator = mask_generator
self.mode = mode
self.residual_target = residual_target
self.channel = channel
self.pre_transform = None
self.post_transform = None
if transform is not None:
self.pre_transform = []
self.post_transform = []
for t in transform.transforms:
if isinstance(t, (transforms.Grayscale, transforms.ToTensor, transforms.Normalize)):
self.post_transform.append(t)
else:
self.pre_transform.append(t)
self.pre_transform = transforms.Compose(self.pre_transform)
self.post_transform = transforms.Compose(self.post_transform)
self.noise_mode = noise_mode
assert noise_mode in ['gaussian', 'salt', 'pepper', 's&p', 'poisson', 'gaussian+poisson']
self.mean = noise_mean
self.var = noise_var
self.amount = noise_amount
self.file_path = []
file_list = os.listdir(self.root)
for file_name in file_list:
if os.path.isfile(os.path.join(root, file_name)):
self.file_path.append(os.path.join(root, file_name))
if train_test is not None:
length = int(train_test * (len(self.file_path)))
self.file_path = self.file_path[:length] if mode == 'train' else self.file_path[length:]
def __len__(self):
return len(self.file_path)
def __getitem__(self, index):
img = Image.open(self.file_path[index])
img.convert('RGB')
if self.pre_transform is not None:
img = self.pre_transform(img)
img_np = np.array(img)
if isinstance(self.var, (list, tuple)):
var = np.random.rand(1) * (self.var[1] - self.var[0]) + self.var[0]
else:
var = self.var
if self.mode == 'train':
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson')
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson')
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var)
else:
# fixed noise for each image, convenient for validation
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount, seed=1024 + index)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
if self.channel == 1:
noise = (noisy_img - img_np)[:, :, 0]
noise = noise[:, :, np.newaxis]
noisy_img = img_np + noise
noisy_img = Image.fromarray((255 * noisy_img).astype(np.uint8))
if self.transform is not None:
noisy_img = self.transform(noisy_img) if self.post_transform is None else self.post_transform(noisy_img)
img = self.transform(img) if self.post_transform is None else self.post_transform(img)
if self.residual_target:
target = noisy_img - img
else:
target = img
if self.mask_generator is not None:
mask = self.mask_generator()
return noisy_img, target, mask
return noisy_img, target
class DenoisingTestMixFolder(Dataset):
"""Data loader for the denoising mixed test set.
data_root/test_mix/noise_level/imgae.png
type: test_mix
noise_level: 5 (+ 1: ground truth)
captures.png: 48 images in each fov
Args:
noise_levels (seq): e.g. [1, 2, 4] select `raw`, `avg2`, `avg4` folders
"""
def __init__(self, root, loader, noise_levels, transform, target_transform, mask_generator=None):
super().__init__()
all_noise_levels = [1, 2, 4, 8, 16]
assert all([level in all_noise_levels for level in all_noise_levels])
self.noise_levels = noise_levels
self.root = root
self.loader = loader
self.transform = transform
self.target_transform = target_transform
self.samples = self._gather_files()
self.mask_generator = mask_generator
dataset_info = {'Dataset': 'test_mix',
'Noise levels': self.noise_levels,
'# samples': len(self.samples)
}
print(json.dumps(dataset_info, indent=4))
def _gather_files(self):
samples = []
root_dir = os.path.expanduser(self.root)
test_mix_dir = os.path.join(root_dir, 'test_mix')
gt_dir = os.path.join(test_mix_dir, 'gt')
for noise_level in self.noise_levels:
if noise_level == 1:
noise_dir = os.path.join(test_mix_dir, 'raw')
elif noise_level in [2, 4, 8, 16]:
noise_dir = os.path.join(test_mix_dir, f'avg{noise_level}')
for fname in sorted(os.listdir(noise_dir)):
if is_image_file(fname):
noisy_file = os.path.join(noise_dir, fname)
clean_file = os.path.join(gt_dir, fname)
samples.append((noisy_file, clean_file))
return samples
def __getitem__(self, index):
"""
Args:
index (int): Index
Returns:
tuple: (noisy, clean)
"""
noisy_file, clean_file = self.samples[index]
noisy, clean = self.loader(noisy_file), self.loader(clean_file)
if self.transform is not None:
noisy = self.transform(noisy)
if self.target_transform is not None:
clean = self.target_transform(clean)
if self.mask_generator is not None:
mask = self.mask_generator()
return noisy, clean, mask
return noisy, clean
def __len__(self):
return len(self.samples)
class DenoisingFolder(torch.utils.data.Dataset):
"""Class for the denoising dataset for both train and test, with
file structure:
data_root/type/noise_level/fov/capture.png
type: 12
noise_level: 5 (+ 1: ground truth)
fov: 20 (the 19th fov is for testing)
capture.png: 50 images in each fov --> use fewer samples
Args:
root (str): root directory to the dataset
train (bool): Training set if True, else Test set
noise_levels (seq): e.g. [1, 2, 4] select `raw`, `avg2`, `avg4` folders
types (seq, optional): e.g. ['TwoPhoton_BPAE_B', 'Confocal_MICE`]
test_fov (int, optional): default 19. 19th fov is test fov
captures (int): select # images within one folder
transform (callable, optional): A function/transform that takes in
an PIL image and returns a transformed version. E.g, transforms.RandomCrop
target_transform (callable, optional): A function/transform that takes
in the target and transforms it.
loader (callable, optional): image loader
"""
def __init__(self, root, train, noise_levels, types=None, test_fov=19,
captures=2, transform=None, target_transform=None, loader=pil_loader, mask_generator=None):
super().__init__()
all_noise_levels = [1, 2, 4, 8, 16]
all_types = ['TwoPhoton_BPAE_R', 'TwoPhoton_BPAE_G', 'TwoPhoton_BPAE_B',
'TwoPhoton_MICE', 'Confocal_MICE', 'Confocal_BPAE_R',
'Confocal_BPAE_G', 'Confocal_BPAE_B', 'Confocal_FISH',
'WideField_BPAE_R', 'WideField_BPAE_G', 'WideField_BPAE_B']
assert all([level in all_noise_levels for level in all_noise_levels])
self.noise_levels = noise_levels
if types is None:
self.types = all_types
else:
assert all([img_type in all_types for img_type in types])
self.types = types
self.root = root
if train:
fovs = list(range(1, 20 + 1))
fovs.remove(test_fov)
self.fovs = fovs
else:
self.fovs = [test_fov]
self.captures = captures
self.transform = transform
self.target_transform = target_transform
self.loader = loader
self.samples = self._gather_files()
self.mask_generator = mask_generator
dataset_info = {'Dataset': 'train' if train else 'test',
'Noise levels': self.noise_levels,
f'{len(self.types)} Types': self.types,
'Fovs': self.fovs,
'# samples': len(self.samples)
}
print(json.dumps(dataset_info, indent=4))
def _gather_files(self):
samples = []
root_dir = os.path.expanduser(self.root)
# types: microscopy_cell
subdirs = [os.path.join(root_dir, name) for name in os.listdir(root_dir)
if (os.path.isdir(os.path.join(root_dir, name)) and name in self.types)]
for subdir in subdirs:
gt_dir = os.path.join(subdir, 'gt')
for noise_level in self.noise_levels:
if noise_level == 1:
noise_dir = os.path.join(subdir, 'raw')
elif noise_level in [2, 4, 8, 16]:
noise_dir = os.path.join(subdir, f'avg{noise_level}')
for i_fov in self.fovs:
noisy_fov_dir = os.path.join(noise_dir, f'{i_fov}')
clean_file = os.path.join(gt_dir, f'{i_fov}', 'avg50.png')
for fname in sorted(os.listdir(noisy_fov_dir))[:self.captures]:
if is_image_file(fname):
noisy_file = os.path.join(noisy_fov_dir, fname)
samples.append((noisy_file, clean_file))
return samples
def __getitem__(self, index):
"""
Args:
index (int): Index
Returns:
tuple: (noisy, clean)
"""
noisy_file, clean_file = self.samples[index]
noisy, clean = self.loader(noisy_file), self.loader(clean_file)
if self.transform is not None:
noisy = self.transform(noisy)
if self.target_transform is not None:
clean = self.target_transform(clean)
if self.mask_generator is not None:
mask = self.mask_generator()
return noisy, clean, mask
return noisy, clean
def __len__(self):
return len(self.samples)
class DND(NaturalNoise):
def __init__(self, root, transform=None, mask_generator=None):
super(DND, self).__init__(root, transform=transform, mask_generator=mask_generator)
file_list = os.listdir(self.root)
for name in sorted(file_list):
self.samples.append(os.path.join(root, name))
def __getitem__(self, idx):
img = sio.loadmat(self.samples[idx])
x = np.uint8(255 * np.array(img['Inoisy_crop']))
x = Image.fromarray(x, mode='RGB')
if self.transform is not None:
x = self.transform(x)
y = x
if self.mask_generator is not None:
mask = self.mask_generator()
return x, y, mask
return x, y
class CT(Dataset):
def __init__(self, root, mode='train', transform=None, mask_generator=None, residual_target=True,
noise_mode='gaussian', noise_mean=0, noise_var=0.005, noise_amount=0.05):
super().__init__()
self.root = root
self.transform = transform
self.mask_generator = mask_generator
self.mode = mode
self.residual_target = residual_target
self.pre_transform = None
self.post_transform = None
if transform is not None:
self.pre_transform = []
self.post_transform = []
for t in transform.transforms:
if isinstance(t, (transforms.Grayscale, transforms.ToTensor, transforms.Normalize)):
self.post_transform.append(t)
else:
self.pre_transform.append(t)
self.pre_transform = transforms.Compose(self.pre_transform)
self.post_transform = transforms.Compose(self.post_transform)
self.noise_mode = noise_mode
assert noise_mode in ['gaussian', 'salt', 'pepper', 's&p', 'poisson', 'gaussian+poisson']
self.mean = noise_mean
self.var = noise_var
self.amount = noise_amount
self.file = np.load(self.root)
def __len__(self):
return len(self.file)
def __getitem__(self, index):
img = (self.file[index] - np.min(self.file[index])) / np.max(self.file[index])
img = Image.fromarray((255 * img).astype(np.uint8))
img.convert('RGB')
if self.pre_transform is not None:
img = self.pre_transform(img)
img_np = np.array(img)
if isinstance(self.var, (list, tuple)):
var = np.random.rand(1) * (self.var[1] - self.var[0]) + self.var[0]
else:
var = self.var
if self.mode == 'train':
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson')
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson')
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var)
else:
# fixed noise for each image, convenient for validation
if self.noise_mode == 'gaussian':
noisy_img = random_noise(img_np, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
elif self.noise_mode == 's&p' or self.noise_mode == 'salt' or self.noise_mode == 'pepper':
noisy_img = random_noise(img_np, mode=self.noise_mode, amount=self.amount, seed=1024 + index)
elif self.noise_mode == 'poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
elif self.noise_mode == 'gaussian+poisson':
noisy_img = random_noise(img_np, mode='poisson', seed=1024 + index)
noisy_img = random_noise(noisy_img, mode='gaussian', mean=self.mean, var=var, seed=1024 + index)
noisy_img = Image.fromarray((255 * noisy_img).astype(np.uint8))
if self.transform is not None:
noisy_img = self.transform(noisy_img) if self.post_transform is None else self.post_transform(noisy_img)
img = self.transform(img) if self.post_transform is None else self.post_transform(img)
if self.residual_target:
target = noisy_img - img
else:
target = img
if self.mask_generator is not None:
mask = self.mask_generator()
return noisy_img, target, mask
return noisy_img, target