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utils.py
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from datetime import datetime
import numpy as np
import os
import shutil
import math
import random
import torch
import torch.nn as nn
import torchvision
from numpy.random import default_rng
from sklearn.metrics import precision_recall_fscore_support, classification_report, confusion_matrix, roc_auc_score, \
pairwise_distances
from torch.optim.lr_scheduler import LambdaLR
from torch.utils.data import DataLoader
from data.dataset_utils import WeaklySupervisedDataset
from model.densenet import densenet121
from model.lenet import LeNet
from model.loss_net import LossNet
from model.resnet import resnet18
from model.resnet_autoencoder import ResnetAutoencoder
from model.simclr_arch import SimCLRArch
from model.wideresnet import WideResNet
from augmentations.randaugment import RandAugmentMC
import torch.nn.functional as F
import torchvision.models as models
def save_checkpoint(args, state, is_best, filename='checkpoint.pth.tar', best_model_filename='model_best.pth.tar'):
directory = os.path.join(args.checkpoint_path, f'{args.name}_{args.seed}')
if not os.path.exists(directory):
os.makedirs(directory)
filename = os.path.join(directory, filename)
torch.save(state, filename)
if is_best:
shutil.copyfile(filename, os.path.join(directory, best_model_filename))
class AverageMeter(object):
def __init__(self):
self.val = 0
self.avg = 0
self.sum = 0
self.count = 0
def reset(self):
self.val = 0
self.avg = 0
self.sum = 0
self.count = 0
def update(self, val, n=1):
self.val = val
self.sum += val * n
self.count += n
self.avg = self.sum / self.count
class LossPerClassMeter(object):
def __init__(self, classes_num):
self.classes_num = classes_num
self.avg = [0 for _ in range(classes_num)]
self.sum = [0 for _ in range(classes_num)]
self.count = [0 for _ in range(classes_num)]
def reset(self):
self.avg = [0 for _ in range(self.classes_num)]
self.sum = [0 for _ in range(self.classes_num)]
self.count = [0 for _ in range(self.classes_num)]
def update(self, losses, targets):
for i in range(self.classes_num):
self.sum[i] += np.sum(losses[targets == i])
self.count[i] += np.sum(targets == i)
# noinspection PyTypeChecker
self.avg[i] = self.sum[i] / (self.count[i] + 1e-6)
class View(nn.Module):
def __init__(self, shape):
super(View, self).__init__()
self.shape = shape
def forward(self, x):
batch_size = x.shape[0]
x = x.view(batch_size, *self.shape)
return x
class Flatten(nn.Module):
def __init__(self):
super(Flatten, self).__init__()
def forward(self, x):
batch_size = x.shape[0]
return x.view(batch_size, -1)
def accuracy(output, target, topk=(1,)):
maxk = max(topk)
batch_size = target.size(0)
_, pred = output.topk(maxk, 1, True, True)
pred = pred.t()
correct = pred.eq(target.view(1, -1).expand_as(pred))
res = []
for k in topk:
correct_k = correct[:k].reshape(-1).float().sum(0)
res.append(correct_k.mul_(100.0 / batch_size))
return res
def create_loaders(args, labeled_dataset, unlabeled_dataset, test_dataset, labeled_indices, unlabeled_indices, kwargs,
unlabeled_subset_num):
labeled_dataset.indices = labeled_indices
random.shuffle(unlabeled_indices)
unlabeled_dataset.indices = unlabeled_indices[:unlabeled_subset_num]
labeled_loader = DataLoader(dataset=labeled_dataset, batch_size=args.batch_size, shuffle=True, **kwargs)
unlabeled_loader = DataLoader(dataset=unlabeled_dataset, batch_size=args.batch_size, shuffle=False, **kwargs)
val_loader = DataLoader(dataset=test_dataset, batch_size=args.batch_size, shuffle=True, **kwargs)
return labeled_loader, unlabeled_loader, val_loader
def create_base_loader(base_dataset, kwargs, batch_size):
return DataLoader(dataset=base_dataset, batch_size=batch_size, drop_last=True, shuffle=True, **kwargs)
def random_sampling(unlabeled_indices, number):
rng = default_rng()
samples_indices = rng.choice(unlabeled_indices.shape[0], size=number, replace=False)
return samples_indices
def postprocess_indices(labeled_indices, unlabeled_indices, samples_indices):
unlabeled_mask = torch.ones(size=(len(unlabeled_indices),), dtype=torch.bool)
samples_indices = samples_indices[samples_indices < len(unlabeled_indices)]
unlabeled_mask[samples_indices] = 0
labeled_indices = np.hstack([labeled_indices, unlabeled_indices[~unlabeled_mask]])
unlabeled_indices = unlabeled_indices[unlabeled_mask]
return labeled_indices, unlabeled_indices
class Metrics:
def __init__(self):
self.targets = []
self.outputs = []
self.outputs_probs = None
def add_mini_batch(self, mini_targets, mini_outputs):
self.targets.extend(mini_targets.tolist())
self.outputs.extend(torch.argmax(mini_outputs, dim=1).tolist())
self.outputs_probs = mini_outputs \
if self.outputs_probs is None else torch.cat([self.outputs_probs, mini_outputs], dim=0)
def get_metrics(self, average='macro'):
return precision_recall_fscore_support(self.targets, self.outputs, average=average, zero_division=1)
def get_report(self, target_names):
return classification_report(self.targets, self.outputs,
zero_division=1, output_dict=True, target_names=target_names)
def get_confusion_matrix(self):
return confusion_matrix(self.targets, self.outputs)
def get_roc_auc_curve(self):
self.outputs_probs = torch.softmax(self.outputs_probs, dim=1)
return roc_auc_score(self.targets, self.outputs_probs.cpu().numpy(), multi_class='ovr')
class NTXent(nn.Module):
def __init__(self, batch_size, temperature, device):
super(NTXent, self).__init__()
self.temperature = temperature
self.device = device
self.criterion = nn.CrossEntropyLoss(reduction="sum")
self.similarity_f = nn.CosineSimilarity(dim=2)
self.batch_size = batch_size
self.mask = self.mask_correlated_samples()
def mask_correlated_samples(self):
# noinspection PyTypeChecker
mask = torch.ones((self.batch_size * 2, self.batch_size * 2), dtype=bool)
mask = mask.fill_diagonal_(0)
for i in range(self.batch_size):
mask[i, self.batch_size + i] = 0
mask[self.batch_size + i, i] = 0
return mask
def forward(self, z_i, z_j):
p1 = torch.cat((z_i, z_j), dim=0)
sim = self.similarity_f(p1.unsqueeze(1), p1.unsqueeze(0)) / self.temperature
sim_i_j = torch.diag(sim, self.batch_size)
sim_j_i = torch.diag(sim, -self.batch_size)
positive_samples = torch.cat((sim_i_j, sim_j_i), dim=0).reshape(
self.batch_size * 2, 1
)
negative_samples = sim[self.mask].reshape(self.batch_size * 2, -1)
labels = torch.zeros(self.batch_size * 2).to(self.device).long()
logits = torch.cat((positive_samples, negative_samples), dim=1)
loss = self.criterion(logits, labels)
loss /= 2 * self.batch_size
return loss
class TransformsSimCLR:
def __init__(self, size):
s = 1
color_jitter = torchvision.transforms.ColorJitter(
0.8 * s, 0.8 * s, 0.8 * s, 0.2 * s
)
self.train_transform = torchvision.transforms.Compose(
[
torchvision.transforms.RandomResizedCrop(size=size),
torchvision.transforms.RandomHorizontalFlip(),
torchvision.transforms.RandomApply([color_jitter], p=0.8),
torchvision.transforms.RandomGrayscale(p=0.2),
torchvision.transforms.ToTensor(),
]
)
self.test_transform = torchvision.transforms.Compose(
[
torchvision.transforms.Resize(size=(size, size)),
torchvision.transforms.ToTensor(),
]
)
def __call__(self, x):
return self.train_transform(x), self.train_transform(x)
class TransformFix(object):
def __init__(self, input_size=32, crop_size=32):
self.weak = torchvision.transforms.Compose([
torchvision.transforms.RandomHorizontalFlip(),
torchvision.transforms.RandomCrop(size=crop_size, padding=int(crop_size * 0.125), padding_mode='reflect'),
torchvision.transforms.Resize(size=input_size),
torchvision.transforms.ToTensor(),
])
self.strong = torchvision.transforms.Compose([
torchvision.transforms.RandomHorizontalFlip(),
torchvision.transforms.RandomCrop(size=crop_size, padding=int(crop_size * 0.125), padding_mode='reflect'),
RandAugmentMC(n=2, m=10),
torchvision.transforms.Resize(size=input_size),
torchvision.transforms.ToTensor(),
])
def __call__(self, x):
weak = self.weak(x)
strong = self.strong(x)
return weak, strong
def create_model_optimizer_scheduler(args, dataset_class, optimizer='adam', scheduler='steplr',
load_optimizer_scheduler=False):
if args.arch == 'wideresnet':
model = WideResNet(depth=args.layers,
num_classes=dataset_class.num_classes,
widen_factor=args.widen_factor,
dropout_rate=args.drop_rate)
elif args.arch == 'densenet':
model = densenet121(num_classes=dataset_class.num_classes)
elif args.arch == 'lenet':
model = LeNet(num_channels=3, num_classes=dataset_class.num_classes,
droprate=args.drop_rate, input_size=dataset_class.input_size)
elif args.arch == 'resnet':
model = resnet18(num_classes=dataset_class.num_classes, input_size=dataset_class.input_size,
drop_rate=args.drop_rate)
else:
raise NotImplementedError
print('Number of model parameters: {}'.format(
sum([p.data.nelement() for p in model.parameters()])))
model = model.cuda()
if optimizer == 'adam':
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
else:
optimizer = torch.optim.SGD(model.parameters(), lr=args.lr, momentum=args.momentum,
nesterov=args.nesterov, weight_decay=args.weight_decay)
if scheduler == 'steplr':
scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=50, gamma=0.2)
else:
args.iteration = args.fixmatch_k_img // args.batch_size
args.total_steps = args.fixmatch_epochs * args.iteration
scheduler = get_cosine_schedule_with_warmup(
optimizer, args.fixmatch_warmup * args.iteration, args.total_steps)
if args.resume:
if load_optimizer_scheduler:
model, optimizer, scheduler = resume_model(args, model, optimizer, scheduler)
else:
model, _, _ = resume_model(args, model)
return model, optimizer, scheduler
def create_model_optimizer_simclr(args, dataset_class):
model = SimCLRArch(num_channels=3,
num_classes=dataset_class.num_classes,
drop_rate=args.drop_rate, normalize=True, arch=args.simclr_arch,
input_size=dataset_class.input_size)
model = model.cuda()
if args.simclr_resume:
model, _, _ = resume_model(args, model)
args.start_epoch = args.simclr_train_epochs
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
scheduler = None
return model, optimizer, scheduler, args
def create_model_optimizer_autoencoder(args, dataset_class):
model = ResnetAutoencoder(z_dim=args.autoencoder_z_dim, num_classes=dataset_class.num_classes,
drop_rate=args.drop_rate, input_size=dataset_class.input_size)
model = model.cuda()
if args.autoencoder_resume:
model, _, _ = resume_model(args, model)
args.start_epoch = args.autoencoder_train_epochs
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
return model, optimizer, args
def create_model_optimizer_loss_net():
model = LossNet().cuda()
optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
return model, optimizer
def get_loss(args, labeled_class_samples, reduction='mean'):
if args.loss == 'ce':
if args.weighted:
classes_weights = np.clip(np.sum(labeled_class_samples) / np.array(labeled_class_samples),
a_min=1, a_max=50)
# noinspection PyArgumentList
criterion = nn.CrossEntropyLoss(weight=torch.FloatTensor(classes_weights).cuda(), reduction=reduction)
else:
criterion = nn.CrossEntropyLoss(reduction=reduction).cuda()
else:
if reduction == 'mean':
criterion = FocalLoss(gamma=2, alpha=0.25, reduction=True)
else:
criterion = FocalLoss(gamma=2, alpha=0.25, reduction=False)
return criterion
def loss_module_objective_func(pred, target, margin=1.0, reduction='mean'):
assert len(pred) % 2 == 0, 'the batch size is not even.'
assert pred.shape == pred.flip(0).shape
pred = (pred - pred.flip(0))[:len(pred) // 2]
target = (target - target.flip(0))[:len(target) // 2]
target = target.detach()
indicator_func = 2 * torch.sign(torch.clamp(target, min=0)) - 1
if reduction == 'mean':
loss = torch.sum(torch.clamp(margin - indicator_func * pred, min=0))
loss = loss / pred.size(0)
elif reduction == 'none':
loss = torch.clamp(margin - indicator_func * pred, min=0)
else:
loss = None
NotImplementedError()
return loss
def resume_model(args, model, optimizer=None, scheduler=None):
if 'simclr' in args.name:
name = f"{args.dataset}@{args.arch}@{'simclr'}"
elif 'auto_encoder' in args.name or 'autoencoder' in args.name:
name = f"{args.dataset}@{args.arch}@{'auto_encoder'}"
else:
name = args.name
file = os.path.join(args.checkpoint_path, name, 'model_best.pth.tar')
if os.path.isfile(file):
print("=> loading checkpoint '{}'".format(file))
checkpoint = torch.load(file)
args.start_epoch = checkpoint['epoch']
model.load_state_dict(checkpoint['state_dict'])
if optimizer:
optimizer.load_state_dict(checkpoint['optimizer'])
if scheduler:
scheduler.load_state_dict(checkpoint['scheduler'])
print("=> loaded checkpoint (epoch {0})".format(checkpoint['epoch']))
else:
print("=> no checkpoint found at '{0}'".format(file))
return model, optimizer, scheduler
def set_model_name(args):
if args.weak_supervision_strategy == 'semi_supervised':
name = f"{args.dataset}@{args.arch}@{args.semi_supervised_method}"
elif args.weak_supervision_strategy == 'active_learning':
name = f"{args.dataset}@{args.arch}@{args.uncertainty_sampling_method}"
else:
name = f"{args.dataset}@{args.arch}@{args.weak_supervision_strategy}"
name = f'{name}{f"_{args.semi_supervised_uncertainty_method}" if "_with_al" in name else ""}'
name = f'{name}{"_pretrained" if args.load_pretrained else ""}'
name = f'{name}{"_k_medoids_100" if args.k_medoids else ""}'
name = f'{name}{"_novel_class_detection" if args.novel_class_detection else ""}'
name = f'{name}{f"_{args.semi_supervised_init}" if args.semi_supervised_init is not None else ""}'
return name
def perform_sampling(args, uncertainty_sampler, epoch, model, train_loader, unlabeled_loader, dataset_class,
labeled_indices, unlabeled_indices, labeled_dataset, unlabeled_dataset, test_dataset, kwargs,
current_labeled):
print(args.weak_supervision_strategy)
subset_num = dataset_class.unlabeled_subset_num
if args.weak_supervision_strategy == 'active_learning':
samples_indices = uncertainty_sampler.get_samples(epoch, args, model,
train_loader,
unlabeled_loader,
num_classes=dataset_class.num_classes,
num_unlabeled=min(subset_num, len(unlabeled_indices)),
number=dataset_class.add_labeled)
print(f'Uncertainty Sampling\t '
f'Current labeled ratio: {current_labeled + args.add_labeled}\t'
f'Model Reset')
elif args.weak_supervision_strategy == 'random_sampling':
samples_indices = random_sampling(unlabeled_indices, number=dataset_class.add_labeled)
print(f'Random Sampling\t '
f'Current labeled ratio: {current_labeled + args.add_labeled}\t'
f'Model Reset')
else:
samples_indices = uncertainty_sampler.get_samples(epoch, args, model,
train_loader,
unlabeled_loader,
num_classes=dataset_class.num_classes,
num_unlabeled=min(subset_num, len(unlabeled_indices)),
number=dataset_class.add_labeled)
print(f'Semi Supervised with Active Learning Sampling\t '
f'Current labeled ratio: {current_labeled + args.add_labeled}\t'
f'Model Reset')
labeled_indices, unlabeled_indices = postprocess_indices(labeled_indices, unlabeled_indices,
samples_indices)
if args.oversampling:
labeled_indices = oversampling_indices(labeled_indices,
np.array(labeled_dataset.targets)[labeled_indices])
train_loader, unlabeled_loader, val_loader = create_loaders(args, labeled_dataset, unlabeled_dataset,
test_dataset, labeled_indices,
unlabeled_indices, kwargs,
dataset_class.unlabeled_subset_num)
return train_loader, unlabeled_loader, val_loader, labeled_indices, unlabeled_indices
def get_cosine_schedule_with_warmup(optimizer,
num_warmup_steps,
num_training_steps,
num_cycles=7. / 16.,
last_epoch=-1):
def _lr_lambda(current_step):
if current_step < num_warmup_steps:
return float(current_step) / float(max(1, num_warmup_steps))
no_progress = float(current_step - num_warmup_steps) / float(max(1, num_training_steps - num_warmup_steps))
return max(0., math.cos(math.pi * num_cycles * no_progress))
# noinspection PyTypeChecker
return LambdaLR(optimizer, _lr_lambda, last_epoch)
# noinspection PyTypeChecker
def oversampling_indices(indices, targets):
oversampled_indices = []
num_classes = []
masks = []
for t in np.unique(targets).tolist():
mask = targets == t
masks.append(mask)
num_classes.append(np.sum(mask))
max_class = np.amax(num_classes)
for i, t in enumerate(np.unique(targets).tolist()):
factor = int(max_class / num_classes[i])
oversampled_indices.extend(np.tile(indices[masks[i]], factor).tolist())
return np.array(oversampled_indices)
def merge(base_dataset, merge_classes):
base_targets = np.array(base_dataset.targets)
base_classes = base_dataset.classes
base_class_to_idx = base_dataset.class_to_idx
for m in merge_classes:
class_idx = []
for c in m:
class_idx.append(base_class_to_idx[c])
class_idx = sorted(class_idx, reverse=True)
min_i = class_idx[-1]
class_name = base_classes[min_i]
for i in class_idx[:-1]:
base_targets[base_targets == i] = min_i
class_name += '_'
for j in range(i + 1, len(base_classes)):
base_targets[base_targets == j] = j - 1
base_class_to_idx[base_classes[j]] = j - 1
class_name += base_classes[i]
del base_class_to_idx[base_classes[i]]
del base_classes[i]
base_class_to_idx[class_name] = base_class_to_idx.pop(base_classes[min_i])
base_classes[min_i] = class_name
base_dataset.targets = base_targets
base_dataset.classes = base_classes
base_dataset.class_to_idx = base_class_to_idx
return base_dataset
def remove(base_dataset, classes_to_remove):
base_targets = np.array(base_dataset.targets)
base_samples = np.array(base_dataset.samples)
base_imgs = np.array(base_dataset.imgs)
classes_to_remove = np.array(classes_to_remove)
base_classes = base_dataset.classes
base_class_to_idx = base_dataset.class_to_idx
base_samples = base_samples[~np.isin(base_targets, classes_to_remove)]
base_imgs = base_imgs[~np.isin(base_targets, classes_to_remove)]
base_targets = base_targets[~np.isin(base_targets, classes_to_remove)]
for r in np.sort(classes_to_remove)[::-1]:
del base_class_to_idx[base_classes[r]]
del base_classes[r]
for i, t in enumerate(np.unique(base_targets)):
base_targets[base_targets == t] = i
base_class_to_idx[base_classes[i]] = i
base_dataset.samples = base_samples.tolist()
base_dataset.targets = base_targets.tolist()
base_dataset.imgs = base_imgs.tolist()
base_dataset.classes = base_classes
base_dataset.class_to_idx = base_class_to_idx
return base_dataset
class FocalLoss(nn.Module):
def __init__(self, gamma=0, alpha=None, reduction=True):
super(FocalLoss, self).__init__()
self.gamma = gamma
self.alpha = alpha
self.size_average = reduction
def forward(self, outputs, data_y):
logpt = - F.cross_entropy(outputs, data_y, reduction='none')
pt = torch.exp(logpt)
# noinspection PyTypeChecker
focal_loss = -((1 - pt) ** self.gamma) * logpt
balanced_focal_loss = self.alpha * focal_loss
if self.size_average:
return balanced_focal_loss.mean()
else:
return balanced_focal_loss
def load_pretrained(model):
model_dict = model.state_dict()
resnet18_pretrained_dict = models.resnet18(pretrained=True).state_dict()
for key in list(model_dict.keys()):
if 'linear' in key or 'conv1.weight' == key:
continue
model_dict[key] = resnet18_pretrained_dict[key.replace('shortcut', 'downsample')]
model.load_state_dict(model_dict)
return model
def class_wise_random_sample(targets, n=1, seed=9999):
targets = np.array(targets)
indices = np.arange(len(targets))
rng = default_rng(seed=seed)
labeled_indices = []
for i in np.unique(targets):
indices_cls = indices[targets == i]
labeled_indices.extend(rng.choice(indices_cls.shape[0], size=n, replace=False).tolist())
return labeled_indices, indices[~np.isin(indices, labeled_indices)]
def k_medoids_init(base_dataset, k_medoids_model, transform_test, mean, std, seed, n, k_medoids_n_clusters):
k_medoids_dataset = WeaklySupervisedDataset(base_dataset, range(len(base_dataset)), transform=transform_test,
mean=mean, std=std)
k_medoids_loader = DataLoader(dataset=k_medoids_dataset, batch_size=128, shuffle=True)
k_medoids_model.eval()
features_h = None
with torch.no_grad():
for i, (data_x, data_y) in enumerate(k_medoids_loader):
data_x = data_x.cuda(non_blocking=True)
h = k_medoids_model.forward_encoder(data_x)
features_h = h if features_h is None else torch.cat([features_h, h], dim=0)
print('K-medoids features: [{0}/{1}]'.format(i, len(k_medoids_loader)))
features_h = features_h.cpu().numpy()
dist_mat = pairwise_distances(features_h)
from sklearn_extra.cluster import KMedoids
k_medoids_clusterer = KMedoids(n_clusters=k_medoids_n_clusters, metric='precomputed', random_state=seed)
k_medoids = k_medoids_clusterer.fit(dist_mat)
indices = np.arange(len(base_dataset))
labeled_indices = []
samples_per_cluster = int(n / k_medoids_n_clusters)
for index in k_medoids.medoid_indices_:
labeled_indices.extend(np.argsort(dist_mat[index])[:samples_per_cluster])
labeled_indices = np.unique(k_medoids.medoid_indices_)
return labeled_indices, indices[~np.isin(indices, labeled_indices)]
def print_args(args):
print('Arguments:\n'
f'Model name: {args.name}\t'
f'Epochs: {args.epochs}\t'
f'Batch Size: {args.batch_size}\n'
f'Architecture: {args.arch}\t'
f'Weak Supervision Strategy: {args.weak_supervision_strategy}\n'
f'Uncertainty Sampling Method: {args.uncertainty_sampling_method}\t'
f'Semi Supervised Method: {args.semi_supervised_method}\n'
f'Dataset root: {args.root}')
def store_logs(args, logs_df, log_type='al_cycles'):
if log_type == 'epoch_wise':
filename = '{0}-{1}-seed:{2}-epoch'.format(datetime.now().strftime("%d.%m.%Y"), args.name, args.seed)
elif log_type == 'ae_loss':
filename = '{0}-{1}-ae-loss'.format(datetime.now().strftime("%d.%m.%Y"), args.name)
elif log_type == 'novel_class':
filename = '{0}-{1}-seed:{2}-class-nums'.format(datetime.now().strftime("%d.%m.%Y"), args.name, args.seed)
else:
filename = '{0}-{1}-seed:{2}'.format(datetime.now().strftime("%d.%m.%Y"), args.name, args.seed)
logs_df.to_csv(os.path.join(args.log_path, filename))