def run_dc(epoch):
end = time.time()
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(train_loader, model, 50000)
# cluster the features
clustering_loss = deepcluster.cluster(features)
# assign pseudo-labels
dataset_train = datasets.CIFAR10('../data',
train=True,
transform=transforms.Compose([
transforms.Pad(4),
transforms.RandomCrop(32),
transforms.RandomHorizontalFlip(),
transforms.ToTensor(),
]))
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset_train)
# uniformly sample per target
sampler = UnifLabelSampler(int(len(train_dataset)),
deepcluster.images_lists)
train_dataloader_new = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch_size,
num_workers=4,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU().cuda())
model.classifier = nn.Sequential(*mlp)
# model.classifier = None
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
print(f'Clustering epoch {epoch} cost time: {time.time() - end} s')
loss = train(train_dataloader_new, model, criterion, optimizer, epoch)
print(f'Train Epoch: {epoch}:\tLoss: {loss}')
def assess_acc(args, test_dataset, test_dataloader, model, num_imgs):
# new clusterer
deepcluster = clustering.__dict__[args.clustering](args.gt_k)
features = compute_features(args, test_dataloader, model, num_imgs)
assess_cluster_loss = deepcluster.cluster(features,
proc_feat=args.proc_feat,
verbose=args.verbose)
# print("images_list sizes of clusterer after cluster")
# for i in xrange(len(deepcluster.images_lists)):
# print("gt_k: %d (%d)" % (i, len(deepcluster.images_lists[i])))
# non shuffled
relabelled_test_dataset = clustering.cluster_assign(args,
deepcluster.images_lists,
test_dataset)
assert (num_imgs == len(test_dataset))
assert (num_imgs == len(relabelled_test_dataset))
# non shuffled
true_labels = np.array([test_dataset[i][1] for i in xrange(num_imgs)])
predicted_labels = np.array(
[relabelled_test_dataset[i][1] for i in xrange(num_imgs)])
assert (true_labels.min() == 0)
assert (true_labels.max() == args.gt_k - 1)
assert (predicted_labels.min() >= 0)
assert (predicted_labels.max() < args.gt_k)
# hungarian matching
num_correct = np.zeros((args.gt_k, args.gt_k))
for i in xrange(num_imgs):
num_correct[predicted_labels[i], true_labels[i]] += 1
match = linear_assignment(num_imgs - num_correct)
reordered_preds = np.zeros(num_imgs, dtype="int")
for pred_i, target_i in match:
reordered_preds[predicted_labels == pred_i] = target_i
distribution, centroid_min_max = analyse(reordered_preds, args.gt_k,
deepcluster.centroids)
acc = compute_acc(reordered_preds, true_labels, args.gt_k)
return acc, distribution, centroid_min_max, assess_cluster_loss
def main():
args_config = args_parser()
config = merge_config(args_config)
train_loader, dev_loader, test_loader, num_train_steps, label_list = load_data(
config)
config.num_train_step = num_train_steps
# reload the model
model, optimizer, device, n_gpu = load_model(config, num_train_steps,
label_list,
args_config.pretrain)
deepcluster = clustering.__dict__[config.clustering](config.num_clusters)
dev_best_acc = 0
dev_best_f1 = 0
test_best_acc = 0
test_best_f1 = 0
for epoch in range(int(config.num_train_epochs)):
print("#######" * 10)
print("EPOCH: ", str(epoch))
features, train_input_ids, train_input_mask, train_segment_ids, train_ner_cate, train_start_pos, train_end_pos \
= compute_features(train_loader, model, len(train_loader), config, device)
clustering_loss, cluster_var = deepcluster.cluster(
features,
config.view_number,
config.cluster_layer,
config.pca_dim,
config.clus_niter,
epoch,
verbose=True)
train_cluster_loader = get_cluster_dataloader(
config, train_input_ids, train_input_mask, train_segment_ids,
train_ner_cate, train_start_pos, train_end_pos)
cluster_dict = clustering.cluster_assign(deepcluster.images_lists)
model, dev_best_acc, dev_best_f1, test_best_acc, test_best_f1 = train_cluster(
model, optimizer, train_cluster_loader, dev_loader, test_loader,
dev_best_acc, dev_best_f1, test_best_acc, test_best_f1, config,
device, n_gpu, label_list, cluster_dict, cluster_var, epoch)
print("=&=" * 15)
print("DEV: current best f1, acc")
print(dev_best_f1, dev_best_acc)
print("TEST: current bes f1, acc")
print(test_best_f1, test_best_acc)
print("=&=" * 15)
def main():
global args
args = parser.parse_args()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
logs = []
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
if args.arch == 'inceptionv1':
model = models.__dict__[args.arch](
sobel=args.sobel,
weight_file='/home/farbod/honours/convert/kit_pytorch.npy')
else:
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
if args.arch == 'inceptionv1':
for key in model.modules():
if isinstance(key, nn.Module): continue
key = torch.nn.DataParallel(key).cuda()
else:
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
#for param in model.parameters():
# param.requires_grad = False
#for param in model.classifier.parameters():
# param.requires_grad = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
#args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
#optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
plot_dir = os.path.join(args.exp, 'plots')
if not os.path.isdir(plot_dir):
os.makedirs(plot_dir)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# preprocessing of data
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
#normalize = transforms.Normalize(mean=[0.5, 0.5, 0.5],
# std=[0.5, 0.5, 0.5])
tra = [
transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(), normalize
]
# load the data
end = time.time()
dataset = datasets.ImageFolder(args.data,
transform=transforms.Compose(tra))
if args.verbose: print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# get ground truth labels for nmi
num_classes = 65
labels = [[] for i in range(num_classes)]
for i, (_, label) in enumerate(dataset.imgs):
labels[label].append(i)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
# cluster the features
clustering_loss, plot, davg = deepcluster.cluster(features,
verbose=args.verbose)
print davg
if epoch < 20:
plot.savefig(os.path.join(plot_dir, 'e{}'.format(epoch)))
# assign pseudo-labels
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
#for i, image in enumerate(train_dataset):
# save_dir = os.path.join('./viz_emb_start', str(image[1]))
# if not os.path.isdir(save_dir):
# os.makedirs(save_dir)
# imn = (image[0].data.cpu().numpy() * 112) + 112
# imn = np.swapaxes(imn, 0, 2)
# imn = np.swapaxes(imn, 1, 0)
# #print imn.astype('uint8')
# #print imn.astype('uint8').shape
# im = Image.fromarray(imn.astype('uint8'))
# im.save(os.path.join(save_dir, '{}.jpg'.format(i)))
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
# print log
if args.verbose:
print(
'###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'.format(epoch,
time.time() - end,
clustering_loss, loss))
nmi_prev = 0
nmi_gt = 0
try:
nmi_prev = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(
nmi_prev))
except IndexError:
pass
nmi_gt = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(labels))
print('NMI against ground-truth labels: {0:.3f}'.format(nmi_gt))
print('####################### \n')
logs.append([epoch, clustering_loss, loss, nmi_prev, nmi_gt, davg])
# save running checkpoint
if (epoch + 1) % 10 == 0 or epoch == 0:
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
},
os.path.join(args.exp,
'checkpoint_{}.pth.tar'.format(epoch + 1)))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
scipy.io.savemat(os.path.join(args.exp, 'logs.mat'),
{'logs': np.array(logs)})
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
print('CNN builded.')
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
print('Optimizer created.')
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in list(checkpoint['state_dict']):
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
epochs_log = Logger(os.path.join(args.exp, 'epochs300'))
# Loading and preprocessing of data: custom Rescale and ToTensor transformations for VidDataset.
# VidDataset has a box_frame, which is a pandas Dataframe containing images path an their bb coordinates.
# Each VidDataset sample is a dict formed by a tensor (the image) and crop_coord (bb xmin, xmax, ymin, ymax).
# If a pickled dataset is passed, it will be deserialized and used, else it will be normally loaded.
# It is useful when we want to preprocess a dataset.
print('Start loading dataset...')
end = time.time()
if args.dataset_pkl:
dataset = deserialize_obj(args.dataset_pkl)
# I will never use labels in deepcluster
dataset.vid_labels = None
else:
tra = [preprocessing.Rescale((224, 224)), preprocessing.ToTensor()]
dataset = VidDataset(xml_annotations_dir=args.ann,
root_dir=args.data,
transform=transforms.Compose(tra))
dataset.imgs = dataset.imgs[0::args.load_step]
dataset.samples = dataset.samples[0::args.load_step]
print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# calculate batch size sum (better clean-up data with clean_data.py)
dataset_len = 0
if not args.dataset_pkl:
dataloader.collate_fn = my_collate
for s in dataloader:
dataset_len += len(s['image'])
else:
dataset_len = len(dataset.imgs)
print("Dataset final dimension: ", dataset_len)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# get the features for the whole dataset hardcoded dataset dim for step=5
features = compute_features(dataloader, model, args.load_step,
dataset_len)
# cluster the features
if args.verbose:
print('Cluster the features')
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
if args.verbose:
print('Assign pseudo labels')
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformly sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
if not args.dataset_pkl:
train_dataloader.collate_fn = my_collate
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'.format(epoch,
time.time() - end,
clustering_loss, loss))
epoch_log = [epoch, time.time() - end, clustering_loss, loss]
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(nmi))
epoch_log.append(nmi)
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
epochs_log.log(epoch_log)
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
device = torch.device('cuda:0' if torch.cuda.is_available() else "cpu")
print(device)
criterion_pseudo = nn.CrossEntropyLoss()
criterion_sup = nn.CrossEntropyLoss(ignore_index=-1,
weight=torch.Tensor([10, 300, 250]).to(
device=device, dtype=torch.double))
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
'''
##########################################
##########################################
# Model definition
##########################################
##########################################'''
model = models.__dict__[args.arch](bn=True,
num_cluster=args.nmb_cluster,
num_category=args.nmb_category)
fd = int(model.cluster_layer[0].weight.size()
[1]) # due to transpose, fd is input dim of W (in dim, out dim)
model.cluster_layer = None
model.category_layer = None
model.features = torch.nn.DataParallel(model.features)
model.to(device, dtype=torch.double)
cudnn.benchmark = True
if args.optimizer is 'Adam':
print('Adam optimizer: conv')
optimizer_body = torch.optim.Adam(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_Adam,
betas=(0.9, 0.999),
weight_decay=10**args.wd,
)
else:
print('SGD optimizer: conv')
optimizer_body = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_SGD,
momentum=args.momentum,
weight_decay=10**args.wd,
)
'''
###############
###############
category_layer
###############
###############
'''
model.category_layer = nn.Sequential(
nn.Linear(fd, args.nmb_category),
nn.Softmax(dim=1),
)
model.category_layer[0].weight.data.normal_(0, 0.01)
model.category_layer[0].bias.data.zero_()
model.category_layer.to(device, dtype=torch.double)
if args.optimizer is 'Adam':
print('Adam optimizer: conv')
optimizer_category = torch.optim.Adam(
filter(lambda x: x.requires_grad,
model.category_layer.parameters()),
lr=args.lr_Adam,
betas=(0.9, 0.999),
weight_decay=10**args.wd,
)
else:
print('SGD optimizer: conv')
optimizer_category = torch.optim.SGD(
filter(lambda x: x.requires_grad,
model.category_layer.parameters()),
lr=args.lr_SGD,
momentum=args.momentum,
weight_decay=10**args.wd,
)
'''
########################################
########################################
Create echogram sampling index
########################################
########################################'''
print('Sample echograms.')
dataset_cp, dataset_semi = sampling_echograms_full_for_comparisonP2(
args) # For comparison (paper #2)
dataloader_cp = torch.utils.data.DataLoader(dataset_cp,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
dataloader_semi = torch.utils.data.DataLoader(dataset_semi,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
dataset_te = sampling_echograms_test_for_comparisonP2()
dataloader_test = torch.utils.data.DataLoader(dataset_te,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
dataset_2019, label_2019, patch_loc = sampling_echograms_2019_for_comparisonP2(
)
dataloader_2019 = torch.utils.data.DataLoader(
dataset_2019,
batch_size=1,
shuffle=False,
num_workers=args.workers,
worker_init_fn=np.random.seed,
drop_last=False,
pin_memory=True)
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster,
args.pca)
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top located layer parameters from checkpoint
copy_checkpoint_state_dict = checkpoint['state_dict'].copy()
for key in list(copy_checkpoint_state_dict):
if 'cluster_layer' in key:
del copy_checkpoint_state_dict[key]
checkpoint['state_dict'] = copy_checkpoint_state_dict
model.load_state_dict(checkpoint['state_dict'])
optimizer_body.load_state_dict(checkpoint['optimizer_body'])
optimizer_category.load_state_dict(
checkpoint['optimizer_category'])
category_save = os.path.join(args.exp, 'category_layer.pth.tar')
if os.path.isfile(category_save):
category_layer_param = torch.load(category_save)
model.category_layer.load_state_dict(category_layer_param)
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
exp_test = os.path.join(args.exp, 'test')
for dir_2 in ['2019', 'pred']:
dir_to_make = os.path.join(exp_test, dir_2)
if not os.path.isdir(dir_to_make):
os.makedirs(dir_to_make)
'''
#######################
#######################
MAIN TRAINING
#######################
#######################'''
for epoch in range(args.start_epoch, args.epochs):
print(
'##################### Start training at Epoch %d ################'
% epoch)
model.classifier = nn.Sequential(
*list(model.classifier.children())
[:-1]) # remove ReLU at classifier [:-1]
model.cluster_layer = None
model.category_layer = None
'''
#######################
#######################
PSEUDO-LABEL GENERATION
#######################
#######################
'''
print('Cluster the features')
features_train, input_tensors_train, labels_train = compute_features_for_comparisonP2(
dataloader_cp,
model,
len(dataset_cp) * args.for_comparisonP2_batchsize,
device=device,
args=args)
clustering_loss, pca_features = deepcluster.cluster(
features_train, verbose=args.verbose)
nan_location = np.isnan(pca_features)
inf_location = np.isinf(pca_features)
if (not np.allclose(nan_location, 0)) or (not np.allclose(
inf_location, 0)):
print('PCA: Feature NaN or Inf found. Nan count: ',
np.sum(nan_location), ' Inf count: ', np.sum(inf_location))
print('Skip epoch ', epoch)
torch.save(pca_features, 'tr_pca_NaN_%d.pth.tar' % epoch)
torch.save(features_train, 'tr_feature_NaN_%d.pth.tar' % epoch)
continue
print('Assign pseudo labels')
size_cluster = np.zeros(len(deepcluster.images_lists))
for i, _list in enumerate(deepcluster.images_lists):
size_cluster[i] = len(_list)
print('size in clusters: ', size_cluster)
img_label_pair_train = zip_img_label(input_tensors_train, labels_train)
train_dataset = clustering.cluster_assign(
deepcluster.images_lists,
img_label_pair_train) # Reassigned pseudolabel
# uniformly sample per target
sampler_train = UnifLabelSampler(int(len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.for_comparisonP2_batchsize, #args.batch
shuffle=False,
num_workers=args.workers,
sampler=sampler_train,
pin_memory=True,
)
'''
####################################################################
####################################################################
TRSNSFORM MODEL FOR SELF-SUPERVISION // SEMI-SUPERVISION
####################################################################
####################################################################
'''
# Recover classifier with ReLU (that is not used in clustering)
mlp = list(model.classifier.children(
)) # classifier that ends with linear(512 * 128). No ReLU at the end
mlp.append(nn.ReLU(inplace=True).to(device))
model.classifier = nn.Sequential(*mlp)
model.classifier.to(device=device, dtype=torch.double)
'''SELF-SUPERVISION (PSEUDO-LABELS)'''
model.category_layer = None
model.cluster_layer = nn.Sequential(
nn.Linear(fd, args.nmb_cluster), # nn.Linear(4096, num_cluster),
nn.Softmax(
dim=1
), # should be removed and replaced by ReLU for category_layer
)
model.cluster_layer[0].weight.data.normal_(0, 0.01)
model.cluster_layer[0].bias.data.zero_()
# model.cluster_layer = model.cluster_layer.double()
model.cluster_layer.to(device=device, dtype=torch.double)
''' train network with clusters as pseudo-labels '''
with torch.autograd.set_detect_anomaly(True):
pseudo_loss, semi_loss, semi_accuracy = semi_train_for_comparisonP2(
train_dataloader,
dataloader_semi,
model,
fd,
criterion_pseudo,
criterion_sup,
optimizer_body,
optimizer_category,
epoch,
device=device,
args=args)
# save checkpoint
if epoch % args.checkpoints == 0:
path = os.path.join(
args.exp,
'checkpoints',
str(epoch) + '_checkpoint.pth.tar',
)
if args.verbose:
print('Save checkpoint at: {0}'.format(path))
torch.save(
{
'epoch': epoch,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer_body': optimizer_body.state_dict(),
'optimizer_category': optimizer_category.state_dict(),
}, path)
torch.save(
model.category_layer.state_dict(),
os.path.join(args.exp, 'checkpoints',
'%d_category_layer.pth.tar' % epoch))
# save running checkpoint
torch.save(
{
'epoch': epoch,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer_body': optimizer_body.state_dict(),
'optimizer_category': optimizer_category.state_dict(),
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
torch.save(model.category_layer.state_dict(),
os.path.join(args.exp, 'category_layer.pth.tar'))
'''
##############
##############
# TEST phase
##############
##############
'''
test_loss, test_accuracy, test_pred, test_label, test_pred_softmax = test_for_comparisonP2(
dataloader_test, model, criterion_sup, device, args)
test_pred_large = rebuild_pred_patch(test_pred)
test_softmax_large = rebuild_pred_patch(test_pred_softmax)
test_label_large = rebuild_pred_patch(test_label)
'''Save prediction of the test set'''
if (epoch % args.save_epoch == 0):
with open(
os.path.join(
args.exp, 'test', 'pred',
'pred_softmax_label_epoch_%d_te.pickle' % epoch),
"wb") as f:
pickle.dump(
[test_pred_large, test_softmax_large, test_label_large], f)
fpr, \
tpr, \
roc_auc, \
roc_auc_macro, \
prob_mat, \
mat, \
f1_score, \
kappa, \
bg_accu, \
se_accu, \
ot_accu = test_analysis(test_pred_large, test_softmax_large, epoch, args)
if os.path.isfile(
os.path.join(args.exp, 'records_te_epoch_patch.pth.tar')):
records_te_epoch = torch.load(
os.path.join(args.exp, 'records_te_epoch_patch.pth.tar'))
else:
records_te_epoch = {
'epoch': [],
'fpr': [],
'tpr': [],
'roc_auc': [],
'roc_auc_macro': [],
'prob_mat': [],
'mat': [],
'f1_score': [],
'kappa': [],
'BG_accu_epoch': [],
'SE_accu_epoch': [],
'OT_accu_epoch': [],
}
records_te_epoch['epoch'].append(epoch)
records_te_epoch['fpr'].append(fpr)
records_te_epoch['tpr'].append(tpr)
records_te_epoch['roc_auc'].append(roc_auc)
records_te_epoch['roc_auc_macro'].append(roc_auc_macro)
records_te_epoch['prob_mat'].append(prob_mat)
records_te_epoch['mat'].append(mat)
records_te_epoch['f1_score'].append(f1_score)
records_te_epoch['kappa'].append(kappa)
records_te_epoch['BG_accu_epoch'].append(bg_accu)
records_te_epoch['SE_accu_epoch'].append(se_accu)
records_te_epoch['OT_accu_epoch'].append(ot_accu)
torch.save(records_te_epoch,
os.path.join(args.exp, 'records_te_epoch_patch.pth.tar'))
'''
##############
##############
# 2019 phase
##############
##############
'''
test_loss_2019, test_accuracy_2019, test_pred_2019, test_label_2019, test_pred_softmax_2019 = test_for_comparisonP2(
dataloader_2019, model, criterion_sup, device, args)
test_pred_large_2019 = rebuild_pred_patch(test_pred_2019)
test_softmax_large_2019 = rebuild_pred_patch(test_pred_softmax_2019)
test_label_large_2019 = rebuild_pred_patch(test_label_2019)
test_and_plot_2019(test_pred_large_2019, test_label_large_2019, epoch,
args)
def main(args):
# fix random seeds
seed(31)
# CNN
model = MobileNetV1(num_classes=100, sobel=True)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
[x for x in model.parameters() if x.requires_grad],
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# creating cluster assignments log
cluster_log = Logger(os.path.join('./image_list_log/', 'clusters'))
end = time.time()
# load the data
dataset = datasets.ImageFolder(root=r'./dataset/train',
transform=transform())
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
print('start train')
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
print(epoch)
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset),
args.batch)
# cluster the feature
clustering_loss = deepcluster.cluster(features)
# assign pseudo-labels
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformly sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch,
args.lr, args.wd)
# print log
# print('###### Epoch [{0}] ###### \n'
# 'Time: {1:.3f} s\n'
# 'Clustering loss: {2:.3f} \n'
# 'ConvNet loss: {3:.3f}'
# .format(epoch, time.time() - end, clustering_loss, loss))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(nmi))
f = open('result.txt', "a")
f.write('NMI against previous assignment: {0:.3f}'.format(nmi))
f.close()
# print(loss)
except IndexError:
pass
print('####################### \n')
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main():
global args
args = parser.parse_args()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# preprocessing of data
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
tra = [
transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(), normalize
]
# load the data
end = time.time()
dataset = datasets.ImageFolder(args.data,
transform=transforms.Compose(tra))
if args.verbose: print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
# cluster the features
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'.format(epoch,
time.time() - end,
clustering_loss, loss))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(nmi))
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main():
global args
args = parser.parse_args()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
# args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
keys_to_del = []
for key in checkpoint['state_dict']:
if 'top_layer' in key:
keys_to_del.append(key)
for key in keys_to_del:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
# optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# preprocessing of data
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
# tra = [transforms.Resize(256),
# transforms.CenterCrop(224),
# transforms.ToTensor(),
# normalize]
# cf. encoder_clustering.py: already resized to 224x224
tra = [transforms.ToTensor(), normalize]
# load the data
end = time.time()
dataset = datasets.ImageFolder(args.data,
transform=transforms.Compose(tra))
if args.verbose: print('Load dataset: {0:.2f} s'.format(time.time() - end))
print('len(dataset)...............:', len(dataset))
print('DataLoader...')
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
print('...DataLoader')
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children())[:-1])
######################################################################
# get the features for the whole dataset
print('compute_features...')
features = compute_features(dataloader, model, len(dataset))
print('features.shape.:', features.shape)
# cluster the features
print('deepcluster.cluster...')
deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
print('clustering.cluster_assign...')
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
# print('cluster_0: %s' % str(deepcluster.images_lists[0]))
# assert len(features) == len(dataset.imgs)
# for i in deepcluster.images_lists[0]:
# print(i, '---', np.linalg.norm(features[i]))
# print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
print('number of clusters computed: %d' % len(deepcluster.images_lists))
print('pickle clustering objects...')
handle = open(os.path.join(args.exp, "features.obj"), "wb")
pickle.dump(features, handle)
handle.close()
handle = open(os.path.join(args.exp, "train_dataset.obj"), "wb")
pickle.dump(train_dataset, handle)
handle.close()
handle = open(os.path.join(args.exp, "images_lists.obj"), "wb")
pickle.dump(deepcluster.images_lists, handle)
handle.close()
handle = open(os.path.join(args.exp, "dataset_imgs.obj"), "wb")
pickle.dump(dataset.imgs, handle)
handle.close()
print('done.')
def main():
global args
args = parser.parse_args()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})"
.format(args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# preprocessing of data
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
tra = [transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(),
normalize]
# load the data
end = time.time()
dataset = datasets.ImageFolder(args.data, transform=transforms.Compose(tra))
if args.verbose: print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
# cluster the features
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'
.format(epoch, time.time() - end, clustering_loss, loss))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1])
)
print('NMI against previous assignment: {0:.3f}'.format(nmi))
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save({'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer' : optimizer.state_dict()},
os.path.join(args.exp, 'checkpoint.pth.tar'))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
# if args.verbose:
# print('Architecture: {}'.format(args.arch))
# model = load_net('149')
# model = mobilenet_v3_large(pretrained=False, sobel=True, num_classes=100)
model = MobileNetV3_Small(num_classes=100, sobel=True)
# model = alexnet(sobel=True)
# fd = 1000
# print(fd)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# creating cluster assignments log
cluster_log = Logger(os.path.join('./image_list_log/', 'clusters'))
normalize = transforms.Normalize(mean=[0.4914, 0.4822, 0.4465],
std=[0.24703223, 0.24348512, 0.26158784])
# preprocessing of data
tra = [
transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(), normalize
]
# load the data
end = time.time()
dataset = datasets.ImageFolder(r'./dataset/train',
transform=transforms.Compose(tra))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# print(model.classifier)
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
# cluster the features
# if args.verbose:
# print('Cluster the features')
clustering_loss = deepcluster.cluster(features)
# assign pseudo-labels
# if args.verbose:
# print('Assign pseudo labels')
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformly sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
# mlp = list()
# mlp.append(nn.Linear(in_features=1024, out_features=1000, bias=True).cuda())
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
# print(mlp)
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
# print(len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(nmi))
f = open('NMI_result.txt', "a")
f.write('NMI against previous assignment: {0:.3f}'.format(nmi))
f.write(" epoch: %d \n" % epoch)
f.close()
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, r'./exp/checkpoint_mobilenetv3_small.pth.tar')
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main():
global args
args = parser.parse_args()
print('args: >>>>>>>>>')
print(args)
print('<<<<<<<<<<<<<<<')
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
# if args.verbose:
# print('Architecture: {}'.format(args.arch))
# model = models.__dict__[args.arch](sobel=args.sobel)
# model.top_layer = None
# model.features = torch.nn.DataParallel(model.features)
# model.cuda()
cudnn.benchmark = True
# preprocessing of data
# normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])
# tra = [transforms.Resize(224),
# transforms.CenterCrop(224),
# transforms.ToTensor(),
# normalize]
# cf. encoder_clustering.py: already resized to 224x224
# tra = [transforms.ToTensor(), normalize]
# load the data
# end = time.time()
# tile_name = args.tile
# image_folder = os.path.join(args.data, tile_name)
# print('image folder: %s' % image_folder)
# dataset = datasets.ImageFolder(image_folder, transform=transforms.Compose(tra))
# print('Load dataset: {0:.2f} s'.format(time.time() - end))
# print('len(dataset)...............:', len(dataset))
# print('DataLoader...')
# dataloader = torch.utils.data.DataLoader(dataset,
# batch_size=args.batch,
# num_workers=args.workers,
# pin_memory=True)
# print('...DataLoader')
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# remove head
# model.top_layer = None
# model.classifier = nn.Sequential(*list(model.classifier.children())[:-1])
######################################################################
# get the features for the whole dataset
if args.features and os.path.exists(args.features):
handle = open(args.features, "rb")
print('load features from filesystem...: %s' % args.features)
features = pickle.load(handle)
print('... loaded.')
handle.close()
handle = open(args.features_fn, "rb")
print('load features_fn from filesystem...: %s' % args.features_fn)
features_fn = pickle.load(handle)
print('... loaded.')
handle.close()
else:
print('compute_features...')
assert 1 == 0, "not supported at moment"
#features = compute_features(dataloader, model, len(dataset))
#print('...compute_features.')
print('features.shape.:', features.shape)
# cluster the features
print('deepcluster.cluster...')
deepcluster.cluster(features, verbose=args.verbose)
num_in_clusters = 0
for cluster_index, cluster in enumerate(deepcluster.images_lists):
print("cluster %d: %d entries." % (cluster_index, len(cluster)))
num_in_clusters += len(cluster)
# assign pseudo-labels
print('clustering.cluster_assign...')
data = clustering.cluster_assign(deepcluster.images_lists, features_fn)
print('number of clusters computed: %d' % len(deepcluster.images_lists))
file_out = os.path.join(os.path.dirname(args.features_fn),
"fname_pseudolabel.obj")
print('pickle list with pseudolabels to \'%s\'...' % file_out)
handle = open(file_out, "wb")
pickle.dump(data.imgs, handle)
handle.close()
assert num_in_clusters == len(data.imgs)
print("in total %d tuples pickled." % len(data.imgs))
# # cf. also coco_knn.py
# k = int(args.knn)
#
# check_small_clusters(deepcluster, k)
#
# tile_to_10nn = {}
# d = features.shape[1] # dimension
#
# for cluster_index, cluster in enumerate(deepcluster.images_lists):
# print('processing cluster %d -->' % (cluster_index + 1))
# start = time.time()
# #####################################################
#
# # calculate 10-NN for each feature of current cluster
# cluster_feature_ids = cluster
#
# res = faiss.StandardGpuResources()
# flat_config = faiss.GpuIndexFlatConfig()
# flat_config.useFloat16 = False
# flat_config.device = 0
# index = faiss.GpuIndexFlatL2(res, d, flat_config)
#
# num_features = len(cluster_feature_ids)
# cluster_features = np.zeros((num_features, features.shape[1])).astype('float32')
# for ind, id in enumerate(cluster_feature_ids):
# # print(ind, '-', id)
# cluster_features[ind] = features[id]
#
# print('cluster_features.shape = %s' % str(cluster_features.shape))
# index.add(cluster_features)
#
# l2_knn, knn = index.search(cluster_features, k + 1) # +1 because 1st is feature itself
# assert knn.shape[0] == cluster_features.shape[0]
#
# for feature_id in range(num_features):
# for id_nn in range(k + 1): # id_nn: id of current nearest neighbor
# id_into_dataset = cluster_feature_ids[knn[feature_id][id_nn]]
# img_path = dataset.imgs[id_into_dataset][0]
# name = os.path.basename(img_path).replace('_' + tile_name, '')
# if id_nn == 0:
# feature_img_name = name
# knn_list = []
# else:
# l2_dist = l2_knn[feature_id][id_nn]
# tuple = (name, l2_dist)
# knn_list.append(tuple)
# assert len(knn_list) == k
# doAdd = True
# if feature_img_name in tile_to_10nn:
# # special case because of duplicate images in COCO dataset (e.g. 000000000927.jpg und 000000341448.jpg)
# assert knn[feature_id][0] == knn[knn[feature_id][1]][0] \
# and knn[feature_id][1] == knn[knn[feature_id][1]][1], '\n%d\n%s\n%s\n%s' % (feature_id, str(knn[feature_id]), str(l2_knn[feature_id]), str(knn))
# id_into_dataset = cluster_feature_ids[knn[feature_id][1]]
# img_path = dataset.imgs[id_into_dataset][0]
# name_repl = os.path.basename(img_path).replace('_' + tile_name, '')
# print('duplicate images detected, replacing %s with %s...' % (feature_img_name, name_repl))
# feature_img_name = name_repl
# if feature_img_name in tile_to_10nn:
# print( '%s already in tile_to_10nn (size: %d, featured_id: %d)' % (feature_img_name, len(tile_to_10nn), feature_id))
# doAdd = False
#
# if doAdd:
# assert feature_img_name not in tile_to_10nn, '%s already in tile_to_10nn (size: %d, featured_id: %d)' % \
# (feature_img_name, len(tile_to_10nn), feature_id)
# tile_to_10nn[feature_img_name] = knn_list
# else:
# print('skip feature %s altogether...' % feature_img_name)
# doAdd = True
#
# print(('processing cluster %d <-- [{0:.2f}s]' % (cluster_index + 1)).format(time.time() - start))
#
#
# if len(tile_to_10nn) != len(dataset.imgs):
# # assert len(tile_to_10nn) == len(dataset.imgs), '%s vs. %s' % (str(len(tile_to_10nn)), str(len(dataset.imgs)))
# print('len(tile_to_10nn) != len(dataset.imgs): %s vs. %s' % (str(len(tile_to_10nn)), str(len(dataset.imgs))))
# keys = {}
# for img_name in tile_to_10nn.keys():
# keys[img_name] = 1
# for img_path in dataset.imgs:
# name = os.path.basename(img_path[0]).replace('_' + tile_name, '')
# if name in keys:
# del keys[name]
# else:
# print('%s not in tile_to_10nn..' % name)
# print('state of keys after iteration:')
# print(keys)
#
# out_dir = os.path.join(args.exp, tile_name)
# file_out = os.path.join(out_dir, tile_name + "_" + args.knn + "nn.obj")
# print('pickle map object to \'%s\'...' % file_out)
# handle = open(file_out, "wb")
# pickle.dump(tile_to_10nn, handle)
# handle.close()
print('done.')
def main(args):
# fix random seeds
print('start training')
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
now = datetime.now()
# load the data
dataloader, dataset_train, dataloader_val, dataset_val, tsamples = load_data(
args.path, args.bs, train_ratio=0.8, test_ratio=0.2)
#load vgg
model = Models.__dict__["vgg16"](args.sobel) # pretrained weights?
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None # why? do we need it here?
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
losses = np.zeros(args.ep) # loss per epoch, array of size ep x 1
accuracies = np.zeros(args.ep)
losses_val = np.zeros(args.ep)
accuracies_val = np.zeros(args.ep)
labels = [
573, 671
] # move to another location, maybe outside for-loop, outside training method
# for all epochs
for epoch in range(args.ep):
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1]
) # The actual classifier seems missing here, why are just the children added to a list?
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset_train),
args.bs, labels)
features_val = compute_features(dataloader_val, model,
len(dataset_val), args.bs, labels)
print('PCA')
pre_data = preprocessing(model, features)
pre_data_val = preprocessing(model, features_val)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.k)
print('clustering')
deepcluster_val = clustering.__dict__[args.clustering](args.k)
clustering_loss = deepcluster.cluster(pre_data, verbose=args.verbose)
clustering_loss_val = deepcluster_val.cluster(pre_data_val,
verbose=args.verbose)
images_list = deepcluster.images_lists
images_list_val = deepcluster_val.images_lists
# pseudo labels
print('train pseudolabels')
train_dataset = clustering.cluster_assign(images_list, dataset_train)
val_dataset = clustering.cluster_assign(images_list_val, dataset_val)
len_d = len(train_dataset)
len_val = len(val_dataset)
# uniformly sample per target
sampler = UnifLabelSampler(int(args.reassign * len_d), images_list)
sampler2 = UnifLabelSampler(int(args.reassign * len_val),
images_list_val)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.bs,
sampler=sampler,
pin_memory=True,
)
val_dataloader = torch.utils.data.DataLoader(
val_dataset,
batch_size=args.bs,
sampler=sampler2,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(images_list))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
# train network with clusters as pseudo-labels
end = time.time()
losses[epoch], accuracies[epoch] = train(train_dataloader, model,
criterion, optimizer, epoch,
args.lr, args.wd)
print(f'epoch {epoch} ended with loss {losses[epoch]}')
losses_val[epoch], accuracies_val[epoch] = validate(
val_dataloader, model, criterion)
plot_loss_acc(losses[0:epoch], losses[0:epoch], accuracies[0:epoch],
accuracies[0:epoch], now, epoch, args.k, tsamples,
args.ep)
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'.format(epoch,
time.time() - end,
losses[epoch]))
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
},
os.path.join(args.exp,
f'checkpoint_{now}_k{args.k}_ep{epoch}.pth.tar'))
# save cluster assignments
cluster_log.log(images_list)
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
device = torch.device('cuda:0' if torch.cuda.is_available() else "cpu")
print(device)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=False,
bn=True,
out=args.nmb_cluster)
fd = int(model.top_layer[0].weight.size()
[1]) # due to transpose, fd is input dim of W (in dim, out dim)
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model = model.double()
model.to(device)
cudnn.benchmark = True
if args.optimizer is 'Adam':
print('Adam optimizer: conv')
optimizer = torch.optim.Adam(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_Adam,
betas=(0.5, 0.99),
weight_decay=10**args.wd,
)
else:
print('SGD optimizer: conv')
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_SGD,
momentum=args.momentum,
weight_decay=10**args.wd,
)
criterion = nn.CrossEntropyLoss()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
copy_checkpoint_state_dict = checkpoint['state_dict'].copy()
for key in list(copy_checkpoint_state_dict):
if 'top_layer' in key:
del copy_checkpoint_state_dict[key]
checkpoint['state_dict'] = copy_checkpoint_state_dict
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, '../../..', 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, '../../..', 'clusters.pickle'))
# # Create echogram sampling index
print('Sample echograms.')
end = time.time()
dataset_cp = sampling_echograms_full(args)
dataloader_cp = torch.utils.data.DataLoader(dataset_cp,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
if args.verbose:
print('Load dataset: {0:.2f} s'.format(time.time() - end))
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster,
args.pca)
# deepcluster = clustering.Kmeans(no.cluster, dim.pca)
loss_collect = [[], [], [], [], []]
nmi_save = []
# for evaluation
dataset_eval = sampling_echograms_eval(args)
eval_dataloader = torch.utils.data.DataLoader(
dataset_eval,
batch_size=args.batch,
shuffle=False,
num_workers=args.workers,
pin_memory=True,
)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
# remove head
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children()))
# get the features for the whole dataset
features_train, input_tensors_train, labels_train = compute_features(
dataloader_cp, model, len(dataset_cp), device=device, args=args)
# cluster the features
print('Cluster the features')
end = time.time()
clustering_loss, pca_features = deepcluster.cluster(
features_train, verbose=args.verbose)
# deepcluster.cluster(features_train, verbose=args.verbose)
print('Cluster time: {0:.2f} s'.format(time.time() - end))
nan_location = np.isnan(pca_features)
inf_location = np.isinf(pca_features)
if (not np.allclose(nan_location, 0)) or (not np.allclose(
inf_location, 0)):
print('PCA: Feature NaN or Inf found. Nan count: ',
np.sum(nan_location), ' Inf count: ', np.sum(inf_location))
print('Skip epoch ', epoch)
torch.save(pca_features, 'pca_NaN_%d.pth.tar' % epoch)
torch.save(features_train, 'feature_NaN_%d.pth.tar' % epoch)
continue
# save patches per epochs
cp_epoch_out = [
features_train, deepcluster.images_lists,
deepcluster.images_dist_lists, input_tensors_train, labels_train
]
linear_svc = SimpleClassifier(epoch,
cp_epoch_out,
tr_size=5,
iteration=20)
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Classify. accu.: {1:.3f} \n'
'Pairwise classify. accu: {2} \n'.format(
epoch, linear_svc.whole_score, linear_svc.pair_score))
if (epoch % args.save_epoch == 0):
end = time.time()
with open(
os.path.join(args.exp, '../../..',
'cp_epoch_%d.pickle' % epoch), "wb") as f:
pickle.dump(cp_epoch_out, f)
with open(
os.path.join(args.exp, '../../..',
'pca_epoch_%d.pickle' % epoch), "wb") as f:
pickle.dump(pca_features, f)
print('Feature save time: {0:.2f} s'.format(time.time() - end))
# assign pseudo-labels
print('Assign pseudo labels')
size_cluster = np.zeros(len(deepcluster.images_lists))
for i, _list in enumerate(deepcluster.images_lists):
size_cluster[i] = len(_list)
print('size in clusters: ', size_cluster)
img_label_pair_train = zip_img_label(input_tensors_train, labels_train)
train_dataset = clustering.cluster_assign(
deepcluster.images_lists,
img_label_pair_train) # Reassigned pseudolabel
# uniformly sample per target
sampler_train = UnifLabelSampler(int(len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
shuffle=False,
num_workers=args.workers,
sampler=sampler_train,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children()
) # classifier that ends with linear(512 * 128)
mlp.append(nn.ReLU().to(device))
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Sequential(
nn.Linear(fd, args.nmb_cluster),
nn.Softmax(dim=1),
)
# model.top_layer = nn.Linear(fd, args.nmb_cluster)
model.top_layer[0].weight.data.normal_(0, 0.01)
model.top_layer[0].bias.data.zero_()
model.top_layer = model.top_layer.double()
model.top_layer.to(device)
# train network with clusters as pseudo-labels
end = time.time()
with torch.autograd.set_detect_anomaly(True):
# loss, tr_epoch_out = train(train_dataloader, model, criterion, optimizer, epoch, device=device, args=args)
loss = train(train_dataloader,
model,
criterion,
optimizer,
epoch,
device=device,
args=args)
print('Train time: {0:.2f} s'.format(time.time() - end))
# if (epoch % args.save_epoch == 0):
# end = time.time()
# with open(os.path.join(args.exp, '..', 'tr_epoch_%d.pickle' % epoch), "wb") as f:
# pickle.dump(tr_epoch_out, f)
# print('Save train time: {0:.2f} s'.format(time.time() - end))
# Accuracy with training set (output vs. pseudo label)
# accuracy_tr = np.mean(tr_epoch_out[1] == np.argmax(tr_epoch_out[2], axis=1))
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'ConvNet tr_loss: {2:.3f} \n'
'Clustering loss: {3:.3f} \n'.format(epoch,
time.time() - end, loss,
clustering_loss))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
nmi_save.append(nmi)
print('NMI against previous assignment: {0:.3f}'.format(nmi))
with open("./nmi_collect.pickle", "wb") as ff:
pickle.dump(nmi_save, ff)
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, '../../..', 'checkpoint.pth.tar'))
# evaluation: echogram reconstruction
if (epoch % args.save_epoch == 0):
eval_epoch_out = evaluate(eval_dataloader,
model,
device=device,
args=args)
with open(
os.path.join(args.exp, '../../..',
'eval_epoch_%d.pickle' % epoch), "wb") as f:
pickle.dump(eval_epoch_out, f)
print('epoch: ', type(epoch), epoch)
print('loss: ', type(loss), loss)
print('linear_svc.whole_score: ', type(linear_svc.whole_score),
linear_svc.whole_score)
print('linear_svc.pair_score: ', type(linear_svc.pair_score),
linear_svc.pair_score)
print('clustering_loss: ', type(clustering_loss), clustering_loss)
loss_collect[0].append(epoch)
loss_collect[1].append(loss)
loss_collect[2].append(linear_svc.whole_score)
loss_collect[3].append(linear_svc.pair_score)
loss_collect[4].append(clustering_loss)
with open(os.path.join(args.exp, '../../..', 'loss_collect.pickle'),
"wb") as f:
pickle.dump(loss_collect, f)
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main():
global args
args = parser.parse_args()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=args.sobel)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10**args.wd,
)
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# preprocessing of data
tra = [transforms.ToTensor(), transforms.Normalize((0.1307, ), (0.3081, ))]
# load the data
end = time.time()
# MNIST-full begin:-------------------------------------------
dataset = datasets.MNIST('./data',
train=True,
download=True,
transform=transforms.Compose(tra))
true_label = dataset.train_labels.cpu().numpy()
# MNIST-full end:-------------------------------------------
# # FMNIST begin:-------------------------------------------
# dataset = datasets.FashionMNIST('./data/fmnist', train=True, download=True,
# transform=transforms.Compose(tra))
# true_label = dataset.train_labels.cpu().numpy()
# # FMNIST end:-------------------------------------------
# # MNIST-test begin:-------------------------------------------
# dataset = datasets.MNIST('./data', train=False, download=True,
# transform=transforms.Compose(tra))
# true_label = dataset.test_labels.cpu().numpy()
# # MNIST-test end:-------------------------------------------
# dataset = datasets.ImageFolder(args.data, transform=transforms.Compose(tra))
# if args.verbose: print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(
*list(model.classifier.children())[:-1])
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
# cluster the features
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
# train_dataset = clustering.cluster_assign(deepcluster.images_lists,
# dataset.train_data)
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.train_data)
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
# print log
if args.verbose:
# print('###### Epoch [{0}] ###### \n'
# 'Time: {1:.3f} s\n'
# 'Clustering loss: {2:.3f} \n'
# 'ConvNet loss: {3:.3f}'
# .format(epoch, time.time() - end, clustering_loss, loss))
try:
y_pred = clustering.arrange_clustering(
deepcluster.images_lists)
y_last = clustering.arrange_clustering(cluster_log.data[-1])
import metrics
acc = metrics.acc(y_pred, y_last)
nmi = metrics.nmi(y_pred, y_last)
acc_ = metrics.acc(true_label, y_pred)
nmi_ = metrics.nmi(true_label, y_pred)
print(
'ACC=%.4f, NMI=%.4f; Relative ACC=%.4f, Relative NMI=%.4f'
% (acc_, nmi_, acc, nmi))
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
device = torch.device('cuda:0' if torch.cuda.is_available() else "cpu")
print(device)
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
model = models.__dict__[args.arch](sobel=False,
bn=True,
out=args.nmb_cluster)
fd = int(model.top_layer[0].weight.size()
[1]) # due to transpose, fd is input dim of W (in dim, out dim)
model.top_layer = None
model.features = torch.nn.DataParallel(model.features)
model = model.double()
model.to(device)
cudnn.benchmark = True
# create optimizer
# optimizer = torch.optim.SGD(
# filter(lambda x: x.requires_grad, model.parameters()),
# lr=args.lr,
# momentum=args.momentum,
# weight_decay=10**args.wd,
# )
optimizer = torch.optim.Adam(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
betas=(0.5, 0.99),
weight_decay=10**args.wd,
)
criterion = nn.CrossEntropyLoss()
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
copy_checkpoint_state_dict = checkpoint['state_dict'].copy()
for key in list(copy_checkpoint_state_dict):
if 'top_layer' in key:
del copy_checkpoint_state_dict[key]
checkpoint['state_dict'] = copy_checkpoint_state_dict
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, '../checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters.pickle'))
# load dataset (initial echograms)
window_size = [args.window_dim, args.window_dim]
# # Create echogram sampling index
print('Sample echograms.')
end = time.time()
dataset_cp = sampling_echograms_full(args)
dataloader_cp = torch.utils.data.DataLoader(dataset_cp,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
if args.verbose:
print('Load dataset: {0:.2f} s'.format(time.time() - end))
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster,
args.pca)
# deepcluster = clustering.Kmeans(no.cluster, dim.pca)
loss_collect = [[], [], []]
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
# remove head
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children(
))) # End with linear(512*128) in original vgg)
# ReLU in .classfier() will follow later
# get the features for the whole dataset
features_train, input_tensors_train, labels_train = compute_features(
dataloader_cp, model, len(dataset_cp), device=device, args=args)
# cluster the features
print('Cluster the features')
end = time.time()
clustering_loss = deepcluster.cluster(features_train,
verbose=args.verbose)
print('Cluster time: {0:.2f} s'.format(time.time() - end))
# save patches per epochs
if ((epoch + 1) % args.save_epoch == 0):
end = time.time()
cp_epoch_out = [
features_train, deepcluster.images_lists,
deepcluster.images_dist_lists, input_tensors_train,
labels_train
]
with open("./cp_epoch_%d.pickle" % epoch, "wb") as f:
pickle.dump(cp_epoch_out, f)
print('Feature save time: {0:.2f} s'.format(time.time() - end))
# assign pseudo-labels
print('Assign pseudo labels')
size_cluster = np.zeros(len(deepcluster.images_lists))
for i, _list in enumerate(deepcluster.images_lists):
size_cluster[i] = len(_list)
print('size in clusters: ', size_cluster)
img_label_pair_train = zip_img_label(input_tensors_train, labels_train)
train_dataset = clustering.cluster_assign(
deepcluster.images_lists,
img_label_pair_train) # Reassigned pseudolabel
# ((img[imgidx], label[imgidx]), pseudolabel, imgidx)
# N = len(imgidx)
# uniformly sample per target
sampler_train = UnifLabelSampler(int(len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
shuffle=False,
num_workers=args.workers,
sampler=sampler_train,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children()
) # classifier that ends with linear(512 * 128)
mlp.append(nn.ReLU().to(device))
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Sequential(
nn.Linear(fd, args.nmb_cluster),
nn.Softmax(dim=1),
)
# model.top_layer = nn.Linear(fd, args.nmb_cluster)
model.top_layer[0].weight.data.normal_(0, 0.01)
model.top_layer[0].bias.data.zero_()
model.top_layer = model.top_layer.double()
model.top_layer.to(device)
# train network with clusters as pseudo-labels
end = time.time()
with torch.autograd.set_detect_anomaly(True):
loss, tr_epoch_out = train(train_dataloader,
model,
criterion,
optimizer,
epoch,
device=device,
args=args)
print('Train time: {0:.2f} s'.format(time.time() - end))
if ((epoch + 1) % args.save_epoch == 0):
end = time.time()
with open("./tr_epoch_%d.pickle" % epoch, "wb") as f:
pickle.dump(tr_epoch_out, f)
print('Save train time: {0:.2f} s'.format(time.time() - end))
# Accuracy with training set (output vs. pseudo label)
accuracy_tr = np.mean(
tr_epoch_out[1] == np.argmax(tr_epoch_out[2], axis=1))
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet tr_loss: {3:.3f} \n'
'ConvNet tr_acc: {4:.3f} \n'.format(epoch,
time.time() - end,
clustering_loss, loss,
accuracy_tr))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
print('NMI against previous assignment: {0:.3f}'.format(nmi))
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
loss_collect[0].append(epoch)
loss_collect[1].append(loss)
loss_collect[2].append(accuracy_tr)
with open("./loss_collect.pickle", "wb") as f:
pickle.dump(loss_collect, f)
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
def main():
global args
use_cuda = torch.cuda.is_available()
device = torch.device("cuda" if use_cuda else "cpu")
criterion = nn.CrossEntropyLoss()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# CNN
if args.verbose:
print('Architecture: VGGMiniCBR')
model = VGGMiniCBR(num_classes=10)
fd = int(model.top_layer.weight.size()[1])
model.top_layer = None
model.to(device)
cudnn.benchmark = True
# create optimizer
optimizer = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
momentum=args.momentum,
weight_decay=10 ** args.wd,
)
# optimizer = torch.optim.Adam(filter(lambda x: x.requires_grad, model.parameters()))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
cluster_log = Logger(os.path.join(exp_path, 'clusters'))
tra = [
transforms.Grayscale(num_output_channels=1),
transforms.RandomAffine(degrees=5, translate=(0.03, 0.03), scale=(0.95, 1.05), shear=5),
transforms.ToTensor(),
transforms.Normalize((mean_std[use_zca][0],), (mean_std[use_zca][1],))
]
end = time.time()
dataset = datasets.ImageFolder(args.data, transform=transforms.Compose(tra))
if args.verbose:
print('Load dataset: {0:.2f} s'.format(time.time() - end))
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch,
num_workers=args.workers,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.top_layer = None
model.classifier = nn.Sequential(*list(model.classifier.children())[:-1]) # ignoring ReLU layer in classifier
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset), device) # ndarray, (60k, 512) [-0.019, 0.016]
# cluster the features
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
train_dataset = clustering.cluster_assign(deepcluster.images_lists,
dataset.imgs)
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
# set last fully connected layer
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).to(device))
model.classifier = nn.Sequential(*mlp)
model.top_layer = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer.weight.data.normal_(0, 0.01)
model.top_layer.bias.data.zero_()
model.top_layer.to(device)
# train network with clusters as pseudo-labels
end = time.time()
# loss = train(train_dataloader, model, criterion, optimizer, epoch)
loss = train(model, device, train_dataloader, optimizer, epoch, criterion)
# print log
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'
.format(epoch, time.time() - end, clustering_loss, loss))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1])
)
writer.add_scalar('nmi/train', nmi, epoch)
print('NMI against previous assignment: {0:.3f}'.format(nmi))
except IndexError:
pass
print('####################### \n')
# save running checkpoint
torch.save({'epoch': epoch + 1,
'arch': "VGGMiniCBR",
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()},
os.path.join(exp_path, 'checkpoint.pth.tar'))
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
torch.save(model.state_dict(), os.path.join(args.exp, "mnist_cnn.pt"))
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
device = torch.device('cuda:0' if torch.cuda.is_available() else "cpu")
print(device)
criterion = nn.CrossEntropyLoss()
cluster_log = Logger(os.path.join(args.exp, '../..', 'clusters.pickle'))
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
'''
##########################################
##########################################
# Model definition
##########################################
##########################################'''
model = models.__dict__[args.arch](bn=True,
num_cluster=args.nmb_cluster,
num_category=args.nmb_category)
fd = int(model.cluster_layer[0].weight.size()
[1]) # due to transpose, fd is input dim of W (in dim, out dim)
model.cluster_layer = None
model.category_layer = None
model.features = torch.nn.DataParallel(model.features)
model = model.double()
model.to(device)
cudnn.benchmark = True
if args.optimizer is 'Adam':
print('Adam optimizer: conv')
optimizer_body = torch.optim.Adam(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_Adam,
betas=(0.9, 0.999),
weight_decay=10**args.wd,
)
else:
print('SGD optimizer: conv')
optimizer_body = torch.optim.SGD(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr_SGD,
momentum=args.momentum,
weight_decay=10**args.wd,
)
'''
###############
###############
category_layer
###############
###############
'''
model.category_layer = nn.Sequential(
nn.Linear(fd, args.nmb_category),
nn.Softmax(dim=1),
)
model.category_layer[0].weight.data.normal_(0, 0.01)
model.category_layer[0].bias.data.zero_()
model.category_layer = model.category_layer.double()
model.category_layer.to(device)
if args.optimizer is 'Adam':
print('Adam optimizer: conv')
optimizer_category = torch.optim.Adam(
filter(lambda x: x.requires_grad,
model.category_layer.parameters()),
lr=args.lr_Adam,
betas=(0.9, 0.999),
weight_decay=10**args.wd,
)
else:
print('SGD optimizer: conv')
optimizer_category = torch.optim.SGD(
filter(lambda x: x.requires_grad,
model.category_layer.parameters()),
lr=args.lr_SGD,
momentum=args.momentum,
weight_decay=10**args.wd,
)
'''
########################################
########################################
Create echogram sampling index
########################################
########################################'''
print('Sample echograms.')
dataset_cp, dataset_semi = sampling_echograms_full(args)
dataloader_cp = torch.utils.data.DataLoader(dataset_cp,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
dataloader_semi = torch.utils.data.DataLoader(dataset_semi,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
dataset_test = sampling_echograms_test(args)
dataloader_test = torch.utils.data.DataLoader(dataset_test,
shuffle=False,
batch_size=args.batch,
num_workers=args.workers,
drop_last=False,
pin_memory=True)
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster,
args.pca)
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top located layer parameters from checkpoint
copy_checkpoint_state_dict = checkpoint['state_dict'].copy()
for key in list(copy_checkpoint_state_dict):
if 'cluster_layer' in key:
del copy_checkpoint_state_dict[key]
# if 'category_layer' in key:
# del copy_checkpoint_state_dict[key]
checkpoint['state_dict'] = copy_checkpoint_state_dict
model.load_state_dict(checkpoint['state_dict'])
optimizer_body.load_state_dict(checkpoint['optimizer_body'])
optimizer_category.load_state_dict(
checkpoint['optimizer_category'])
category_save = os.path.join(args.exp, '../..',
'category_layer.pth.tar')
if os.path.isfile(category_save):
category_layer_param = torch.load(category_save)
model.category_layer.load_state_dict(category_layer_param)
print("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# creating checkpoint repo
exp_check = os.path.join(args.exp, '../..', 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
'''
#######################
#######################
PRETRAIN: commented
#######################
#######################'''
# if args.start_epoch < args.pretrain_epoch:
# if os.path.isfile(os.path.join(args.exp, '..', 'pretrain_loss_collect.pickle')):
# with open(os.path.join(args.exp, '..', 'pretrain_loss_collect.pickle'), "rb") as f:
# pretrain_loss_collect = pickle.load(f)
# else:
# pretrain_loss_collect = [[], [], [], [], []]
# print('Start pretraining with %d percent of the dataset from epoch %d/(%d)'
# % (int(args.semi_ratio * 100), args.start_epoch, args.pretrain_epoch))
# model.cluster_layer = None
#
# for epoch in range(args.start_epoch, args.pretrain_epoch):
# with torch.autograd.set_detect_anomaly(True):
# pre_loss, pre_accuracy = supervised_train(loader=dataloader_semi,
# model=model,
# crit=criterion,
# opt_body=optimizer_body,
# opt_category=optimizer_category,
# epoch=epoch, device=device, args=args)
# test_loss, test_accuracy = test(dataloader_test, model, criterion, device, args)
#
# # print log
# if args.verbose:
# print('###### Epoch [{0}] ###### \n'
# 'PRETRAIN tr_loss: {1:.3f} \n'
# 'TEST loss: {2:.3f} \n'
# 'PRETRAIN tr_accu: {3:.3f} \n'
# 'TEST accu: {4:.3f} \n'.format(epoch, pre_loss, test_loss, pre_accuracy, test_accuracy))
# pretrain_loss_collect[0].append(epoch)
# pretrain_loss_collect[1].append(pre_loss)
# pretrain_loss_collect[2].append(test_loss)
# pretrain_loss_collect[3].append(pre_accuracy)
# pretrain_loss_collect[4].append(test_accuracy)
#
# torch.save({'epoch': epoch + 1,
# 'arch': args.arch,
# 'state_dict': model.state_dict(),
# 'optimizer_body': optimizer_body.state_dict(),
# 'optimizer_category': optimizer_category.state_dict(),
# },
# os.path.join(args.exp, '..', 'checkpoint.pth.tar'))
# torch.save(model.category_layer.state_dict(), os.path.join(args.exp, '..', 'category_layer.pth.tar'))
#
# with open(os.path.join(args.exp, '..', 'pretrain_loss_collect.pickle'), "wb") as f:
# pickle.dump(pretrain_loss_collect, f)
#
# if (epoch+1) % args.checkpoints == 0:
# path = os.path.join(
# args.exp, '..',
# 'checkpoints',
# 'checkpoint_' + str(epoch) + '.pth.tar',
# )
# if args.verbose:
# print('Save checkpoint at: {0}'.format(path))
# torch.save({'epoch': epoch + 1,
# 'arch': args.arch,
# 'state_dict': model.state_dict(),
# 'optimizer_body': optimizer_body.state_dict(),
# 'optimizer_category': optimizer_category.state_dict(),
# }, path)
if os.path.isfile(os.path.join(args.exp, '../..', 'loss_collect.pickle')):
with open(os.path.join(args.exp, '../..', 'loss_collect.pickle'),
"rb") as f:
loss_collect = pickle.load(f)
else:
loss_collect = [[], [], [], [], [], [], []]
if os.path.isfile(os.path.join(args.exp, '../..', 'nmi_collect.pickle')):
with open(os.path.join(args.exp, '../..', 'nmi_collect.pickle'),
"rb") as ff:
nmi_save = pickle.load(ff)
else:
nmi_save = []
'''
#######################
#######################
MAIN TRAINING
#######################
#######################'''
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
model.classifier = nn.Sequential(
*list(model.classifier.children())
[:-1]) # remove ReLU at classifier [:-1]
model.cluster_layer = None
model.category_layer = None
'''
#######################
#######################
PSEUDO-LABEL GENERATION
#######################
#######################
'''
print('Cluster the features')
features_train, input_tensors_train, labels_train = compute_features(
dataloader_cp, model, len(dataset_cp), device=device, args=args)
clustering_loss, pca_features = deepcluster.cluster(
features_train, verbose=args.verbose)
nan_location = np.isnan(pca_features)
inf_location = np.isinf(pca_features)
if (not np.allclose(nan_location, 0)) or (not np.allclose(
inf_location, 0)):
print('PCA: Feature NaN or Inf found. Nan count: ',
np.sum(nan_location), ' Inf count: ', np.sum(inf_location))
print('Skip epoch ', epoch)
torch.save(pca_features, 'tr_pca_NaN_%d.pth.tar' % epoch)
torch.save(features_train, 'tr_feature_NaN_%d.pth.tar' % epoch)
continue
print('Assign pseudo labels')
size_cluster = np.zeros(len(deepcluster.images_lists))
for i, _list in enumerate(deepcluster.images_lists):
size_cluster[i] = len(_list)
print('size in clusters: ', size_cluster)
img_label_pair_train = zip_img_label(input_tensors_train, labels_train)
train_dataset = clustering.cluster_assign(
deepcluster.images_lists,
img_label_pair_train) # Reassigned pseudolabel
# uniformly sample per target
sampler_train = UnifLabelSampler(int(len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch,
shuffle=False,
num_workers=args.workers,
sampler=sampler_train,
pin_memory=True,
)
'''
####################################################################
####################################################################
TRSNSFORM MODEL FOR SELF-SUPERVISION // SEMI-SUPERVISION
####################################################################
####################################################################
'''
# Recover classifier with ReLU (that is not used in clustering)
mlp = list(model.classifier.children(
)) # classifier that ends with linear(512 * 128). No ReLU at the end
mlp.append(nn.ReLU(inplace=True).to(device))
model.classifier = nn.Sequential(*mlp)
model.classifier.to(device)
'''SELF-SUPERVISION (PSEUDO-LABELS)'''
model.category_layer = None
model.cluster_layer = nn.Sequential(
nn.Linear(fd, args.nmb_cluster), # nn.Linear(4096, num_cluster),
nn.Softmax(
dim=1
), # should be removed and replaced by ReLU for category_layer
)
model.cluster_layer[0].weight.data.normal_(0, 0.01)
model.cluster_layer[0].bias.data.zero_()
model.cluster_layer = model.cluster_layer.double()
model.cluster_layer.to(device)
''' train network with clusters as pseudo-labels '''
with torch.autograd.set_detect_anomaly(True):
pseudo_loss, semi_loss, semi_accuracy = semi_train(
train_dataloader,
dataloader_semi,
model,
fd,
criterion,
optimizer_body,
optimizer_category,
epoch,
device=device,
args=args)
# save checkpoint
if (epoch + 1) % args.checkpoints == 0:
path = os.path.join(
args.exp,
'../..',
'checkpoints',
'checkpoint_' + str(epoch) + '.pth.tar',
)
if args.verbose:
print('Save checkpoint at: {0}'.format(path))
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer_body': optimizer_body.state_dict(),
'optimizer_category': optimizer_category.state_dict(),
}, path)
'''
##############
##############
# TEST phase
##############
##############
'''
test_loss, test_accuracy, test_pred, test_label = test(
dataloader_test, model, criterion, device, args)
'''Save prediction of the test set'''
if (epoch % args.save_epoch == 0):
with open(
os.path.join(args.exp, '../..',
'sup_epoch_%d_te.pickle' % epoch), "wb") as f:
pickle.dump([test_pred, test_label], f)
if args.verbose:
print('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Pseudo tr_loss: {2:.3f} \n'
'SEMI tr_loss: {3:.3f} \n'
'TEST loss: {4:.3f} \n'
'Clustering loss: {5:.3f} \n'
'SEMI accu: {6:.3f} \n'
'TEST accu: {7:.3f} \n'.format(epoch,
time.time() - end,
pseudo_loss, semi_loss,
test_loss, clustering_loss,
semi_accuracy, test_accuracy))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.images_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
nmi_save.append(nmi)
print('NMI against previous assignment: {0:.3f}'.format(nmi))
with open(
os.path.join(args.exp, '../..', 'nmi_collect.pickle'),
"wb") as ff:
pickle.dump(nmi_save, ff)
except IndexError:
pass
print('####################### \n')
# save cluster assignments
cluster_log.log(deepcluster.images_lists)
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer_body': optimizer_body.state_dict(),
'optimizer_category': optimizer_category.state_dict(),
}, os.path.join(args.exp, '../..', 'checkpoint.pth.tar'))
torch.save(model.category_layer.state_dict(),
os.path.join(args.exp, '../..', 'category_layer.pth.tar'))
loss_collect[0].append(epoch)
loss_collect[1].append(pseudo_loss)
loss_collect[2].append(semi_loss)
loss_collect[3].append(clustering_loss)
loss_collect[4].append(test_loss)
loss_collect[5].append(semi_accuracy)
loss_collect[6].append(test_accuracy)
with open(os.path.join(args.exp, '../..', 'loss_collect.pickle'),
"wb") as f:
pickle.dump(loss_collect, f)
'''
############################
############################
# PSEUDO-LABEL GEN: Test set
############################
############################
'''
model.classifier = nn.Sequential(
*list(model.classifier.children())
[:-1]) # remove ReLU at classifier [:-1]
model.cluster_layer = None
model.category_layer = None
print('TEST set: Cluster the features')
features_te, input_tensors_te, labels_te = compute_features(
dataloader_test,
model,
len(dataset_test),
device=device,
args=args)
clustering_loss_te, pca_features_te = deepcluster.cluster(
features_te, verbose=args.verbose)
mlp = list(model.classifier.children(
)) # classifier that ends with linear(512 * 128). No ReLU at the end
mlp.append(nn.ReLU(inplace=True).to(device))
model.classifier = nn.Sequential(*mlp)
model.classifier.to(device)
nan_location = np.isnan(pca_features_te)
inf_location = np.isinf(pca_features_te)
if (not np.allclose(nan_location, 0)) or (not np.allclose(
inf_location, 0)):
print('PCA: Feature NaN or Inf found. Nan count: ',
np.sum(nan_location), ' Inf count: ', np.sum(inf_location))
print('Skip epoch ', epoch)
torch.save(pca_features_te, 'te_pca_NaN_%d.pth.tar' % epoch)
torch.save(features_te, 'te_feature_NaN_%d.pth.tar' % epoch)
continue
# save patches per epochs
cp_epoch_out = [
features_te, deepcluster.images_lists,
deepcluster.images_dist_lists, input_tensors_te, labels_te
]
if (epoch % args.save_epoch == 0):
with open(
os.path.join(args.exp, '../..',
'cp_epoch_%d_te.pickle' % epoch), "wb") as f:
pickle.dump(cp_epoch_out, f)
with open(
os.path.join(args.exp, '../..',
'pca_epoch_%d_te.pickle' % epoch), "wb") as f:
pickle.dump(pca_features_te, f)
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
run = wandb.init(project='deepcluster4nlp', config=args)
# load the data
end = time.time()
tokenizer = get_tokenizer()
dataset = ImdbDataset(True, tokenizer)
dataloader = get_dataloader(dataset, tokenizer, args.batch)
if args.verbose:
print(('Load dataset: {0:.2f} s'.format(time.time() - end)))
# cluster_lists = [[i*len(dataset)//args.nmb_cluster + j for j in range(len(dataset)//args.nmb_cluster)]
# for i in range(args.nmb_cluster)]
#
# reassigned_dataset = cluster_assign(cluster_lists, dataset)
#
# reassigned_dataloader = get_dataloader(reassigned_dataset, tokenizer)
# CNN
if args.verbose:
print(('Architecture: {}'.format(args.arch)))
model = textcnn(tokenizer, num_class_features=args.num_class_features)
#model = models.__dict__[args.arch](tokenizer)
#fd =int(model.top_layer.weight.size()[1]) # replaced by num_class_features
model.reset_top_layer()
#model.top_layer = None
#model.features = torch.nn.DataParallel(model.features, device_ids=[0])
model.to(device)
cudnn.benchmark = True
# wandb.watch(model)
# create optimizer
optimizer = torch.optim.AdamW(
[x for x in model.parameters() if x.requires_grad], lr=args.lr)
#optimizer = torch.optim.SGD(
# [x for x in model.parameters() if x.requires_grad],
# lr=args.lr,
# momentum=args.momentum,
# weight_decay=10**args.wd
# )
# define loss function
criterion = nn.CrossEntropyLoss().to(device)
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print(("=> loading checkpoint '{}'".format(args.resume)))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
# remove top_layer parameters from checkpoint
for key in copy.deepcopy(checkpoint['state_dict']):
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print(("=> loaded checkpoint '{}' (epoch {})".format(
args.resume, checkpoint['epoch'])))
else:
print(("=> no checkpoint found at '{}'".format(args.resume)))
# creating checkpoint repo
exp_check = os.path.join(args.exp, 'checkpoints')
if not os.path.isdir(exp_check):
os.makedirs(exp_check)
# creating cluster assignments log
cluster_log = Logger(os.path.join(args.exp, 'clusters'))
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.nmb_cluster)
# training convnet with DeepCluster
for epoch in range(args.start_epoch, args.epochs):
end = time.time()
# remove head
model.reset_top_layer() #top_layer = None
# get the features for the whole dataset
features = compute_features(dataloader, model, len(dataset))
should_save = False
if epoch % 50 == 0 or epoch == args.epochs - 1:
should_save = True
if should_save:
# save the features and dataset
wandb_dataset1 = wandb.Artifact(name=f'data', type='dataset')
with wandb_dataset1.new_file(f'data_epoch_{epoch}.csv') as f:
pd.DataFrame(np.asanyarray([d['text'] for d in dataset.data
])).to_csv(f, sep='\t')
run.use_artifact(wandb_dataset1)
wandb_dataset2 = wandb.Artifact(name=f'features', type='dataset')
with wandb_dataset2.new_file(f'features_epoch_{epoch}.csv') as f:
pd.DataFrame(features).to_csv(f, sep='\t')
run.use_artifact(wandb_dataset2)
pd.DataFrame(
np.asanyarray([[d['text'], d['sentiment']]
for d in dataset.data
])).to_csv(f'res/data_epoch_{epoch}.tsv',
sep='\t',
index=None,
header=['text', 'sentiment'])
pd.DataFrame(features).to_csv(f'res/features_epoch_{epoch}.tsv',
sep='\t',
index=None,
header=False)
# cluster the features
if args.verbose:
print('Cluster the features')
clustering_loss = deepcluster.cluster(features, verbose=args.verbose)
# assign pseudo-labels
if args.verbose:
print('Assign pseudo labels')
# train_dataset = clustering.cluster_assign(deepcluster.cluster_lists,
# dataset.data)
train_dataset = clustering.cluster_assign(deepcluster.cluster_lists,
dataset)
# uniformly sample per target
# sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
# deepcluster.cluster_lists)
# train_dataloader = torch.utils.data.DataLoader(
# train_dataset,
# batch_size=args.batch,
# num_workers=args.workers,
# sampler=sampler,
# pin_memory=True,
# )
train_dataloader = get_dataloader(train_dataset, tokenizer, args.batch)
# set last fully connected layer
model.set_top_layer(cluster_list_length=len(deepcluster.cluster_lists))
#model.classifier = nn.Sequential(*mlp)
#model.top_layer = nn.Linear(num_class_features,len(deepcluster.cluster_lists) )
#model.top_layer.weight.data.normal_(0, 0.01)
#model.top_layer.bias.data.zero_()
#model.top_layer.cuda()
# train network with clusters as pseudo-labels
end = time.time()
loss = train(train_dataloader, model, criterion, optimizer, epoch)
summary_dict = {
'time': time.time() - end,
'clustering_loss': clustering_loss,
'convnet_loss': loss,
'clusters': len(deepcluster.cluster_lists)
}
# print log
if args.verbose:
print(('###### Epoch [{0}] ###### \n'
'Time: {1:.3f} s\n'
'Clustering loss: {2:.3f} \n'
'ConvNet loss: {3:.3f}'.format(epoch,
time.time() - end,
clustering_loss, loss)))
try:
nmi = normalized_mutual_info_score(
clustering.arrange_clustering(deepcluster.cluster_lists),
clustering.arrange_clustering(cluster_log.data[-1]))
summary_dict['NMI'] = nmi
print(('NMI against previous assignment: {0:.3f}'.format(nmi)))
except IndexError:
pass
print('####################### \n')
# wandb log
# wandb.log(summary_dict)
# save running checkpoint
torch.save(
{
'epoch': epoch + 1,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
}, os.path.join(args.exp, 'checkpoint.pth.tar'))
if epoch == args.epochs - 1:
model_artifact = wandb.Artifact(name=f'model', type='model')
model_artifact.add_file(
os.path.join(args.exp, 'checkpoint.pth.tar'))
run.use_artifact(model_artifact)
# save cluster assignments
cluster_log.log(deepcluster.cluster_lists)
def main():
global args
args = parser.parse_args()
args.out_dir = os.path.join(args.out_root, str(args.model_ind))
if not os.path.exists(args.out_dir):
os.makedirs(args.out_dir)
if args.resume:
# get old args
old_args = args
reloaded_args_path = os.path.join(old_args.out_dir, "config.pickle")
print("Loading restarting args from: %s" % reloaded_args_path)
with open(reloaded_args_path, "rb") as args_f:
args = pickle.load(args_f)
assert (args.model_ind == old_args.model_ind)
args.resume = True
next_epoch = args.epoch + 1 # indexed from 0, also = num epochs passed
print("stored losses and accs lens %d %d %d, cutting to %d %d %d" %
(len(args.epoch_loss),
len(args.epoch_cluster_dist),
len(args.epoch_acc),
next_epoch,
next_epoch,
next_epoch + 1))
args.epoch_loss = args.epoch_loss[:next_epoch]
args.epoch_assess_cluster_loss = args.epoch_assess_cluster_loss[:next_epoch]
args.epoch_cluster_dist = args.epoch_cluster_dist[:next_epoch]
args.epoch_acc = args.epoch_acc[:(next_epoch + 1)]
if not hasattr(args, "if_stl_dont_use_unlabelled"):
args.if_stl_dont_use_unlabelled = False
else:
args.epoch_acc = []
args.epoch_assess_cluster_loss = []
args.epoch_cluster_dist = []
args.epoch_loss = [] # train loss
args.epoch_distribution = []
args.epoch_centroid_min = []
args.epoch_centroid_max = []
next_epoch = 0
if not args.find_data_stats:
print("args/config:")
print(config_to_str(args))
sys.stdout.flush()
# fix random seeds
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
np.random.seed(args.seed)
# losses and acc
fig, axarr = plt.subplots(4, sharex=False, figsize=(20, 20))
# distr
distr_fig, distr_ax = plt.subplots(3, sharex=False, figsize=(20, 20))
# Data ---------------------------------------------------------------------
if args.dataset == "MNIST":
assert (not args.sobel)
args.input_ch = 1
else:
if args.sobel:
args.input_ch = 2
else:
args.input_ch = 3
# preprocessing of data
tra = []
tra_test = []
if args.rand_crop_sz != -1:
tra += [transforms.RandomCrop(args.rand_crop_sz)]
tra_test += [transforms.CenterCrop(args.rand_crop_sz)]
tra += [transforms.Resize(args.input_sz)]
tra_test += [transforms.Resize(args.input_sz)]
args.data_mean = None # toggled on in cluster_assign
args.data_std = None
if args.normalize and (not args.find_data_stats):
data_mean, data_std = _DATASET_NORM[args.dataset]
args.data_mean = data_mean
args.data_std = data_std
normalize = transforms.Normalize(mean=args.data_mean, std=args.data_std)
tra.append(normalize)
tra_test.append(normalize)
# actual augmentation here
if not (args.dataset == "MNIST"):
tra += [transforms.RandomHorizontalFlip(),
transforms.ColorJitter(brightness=0.4, contrast=0.4,
saturation=0.4, hue=0.125)
]
else:
print("skipping horizontal flipping and jitter")
tra += [transforms.ToTensor()]
tra_test += [transforms.ToTensor()]
tra = transforms.Compose(tra)
tra_test = transforms.Compose(tra_test)
# load the data
dataset, dataloader, test_dataset, test_dataloader = make_data(args,
tra,
tra_test)
if args.find_data_stats:
print(args.dataset)
print("train dataset mean, std: %s, %s" %
compute_data_stats(dataloader, len(dataset)))
print("test dataset mean, std: %s, %s" %
compute_data_stats(test_dataloader, len(test_dataset)))
exit(0)
# Model --------------------------------------------------------------------
# CNN
if args.verbose:
print('Architecture: {}'.format(args.arch))
sys.stdout.flush()
model = models.__dict__[args.arch](sobel=args.sobel, out=args.k,
input_sp_sz=args.input_sz,
input_ch=args.input_ch)
fd = model.dlen
# model.features = torch.nn.DataParallel(model.features)
model.cuda()
cudnn.benchmark = True
# create optimizer
# top layer not created at this point!
assert (model.top_layer is None)
optimizer = torch.optim.Adam(
filter(lambda x: x.requires_grad, model.parameters()),
lr=args.lr,
# momentum=args.momentum,
# weight_decay=10**args.wd,
)
if args.resume:
# remove top_layer parameters from checkpoint
checkpoint = torch.load(os.path.join(old_args.out_dir, "%s.pytorch" %
args.resume_mode))
for key in checkpoint['state_dict']:
if 'top_layer' in key:
del checkpoint['state_dict'][key]
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
# after optimiser loading done, add a top layer
# model.make_top_layer()
# define loss function
criterion = nn.CrossEntropyLoss().cuda()
# clustering algorithm to use
deepcluster = clustering.__dict__[args.clustering](args.k)
if (not args.resume) or args.just_analyse:
print("Doing some assessment")
sys.stdout.flush()
acc, distribution, centroid_min_max, assess_cluster_loss = \
assess_acc(args, test_dataset, test_dataloader, model,
len(test_dataset))
print("got %f" % acc)
sys.stdout.flush()
if args.just_analyse:
exit(0)
args.epoch_acc.append(acc)
args.epoch_assess_cluster_loss.append(assess_cluster_loss)
args.epoch_distribution.append(list(distribution))
args.epoch_centroid_min.append(centroid_min_max[0])
args.epoch_centroid_max.append(centroid_min_max[1])
# Train --------------------------------------------------------------------
for epoch in range(next_epoch, args.total_epochs):
# remove relu (getting features)
# model.remove_feature_head_relu()
# get the features for the whole dataset
features = compute_features(args, dataloader, model, len(dataset))
# cluster the features
clustering_loss = deepcluster.cluster(features,
proc_feat=args.proc_feat,
verbose=args.verbose)
# assign pseudo-labels to make new dataset
train_dataset = clustering.cluster_assign(args,
deepcluster.images_lists,
dataset,
tra=tra)
# uniformely sample per target
sampler = UnifLabelSampler(int(args.reassign * len(train_dataset)),
deepcluster.images_lists)
train_dataloader = torch.utils.data.DataLoader(
train_dataset,
batch_size=args.batch_sz,
num_workers=args.workers,
sampler=sampler,
pin_memory=True,
)
if epoch == next_epoch:
print("fd length: %d" % fd)
# prepare for training by reintroducing relu and resetting last layer
# model.add_feature_head_relu()
# model.reset_top_layer()
# train network with clusters as pseudo-labels
loss = train(train_dataloader, model, criterion, optimizer, epoch,
per_batch=(epoch == next_epoch))
# assess ---------------------------------------------------------------
acc, distribution, centroid_min_max, assess_cluster_loss = \
assess_acc(args, test_dataset, test_dataloader, model, len(test_dataset))
print("Model %d, epoch %d, cluster loss %f, train loss %f, acc %f "
"time %s"
% (args.model_ind, epoch, clustering_loss, loss, acc,
datetime.now()))
sys.stdout.flush()
# update args
is_best = False
if acc > max(args.epoch_acc):
is_best = True
args.epoch_acc.append(acc)
args.epoch_assess_cluster_loss.append(assess_cluster_loss)
args.epoch_loss.append(loss)
args.epoch_cluster_dist.append(clustering_loss)
args.epoch_distribution.append(distribution)
args.epoch_centroid_min.append(centroid_min_max[0])
args.epoch_centroid_max.append(centroid_min_max[1])
# draw graphs and save
axarr[0].clear()
axarr[0].plot(args.epoch_acc)
axarr[0].set_title("Acc")
axarr[1].clear()
axarr[1].plot(args.epoch_loss)
axarr[1].set_title("Training loss")
axarr[2].clear()
axarr[2].plot(args.epoch_cluster_dist)
axarr[2].set_title("Cluster distance (train, k)")
axarr[3].clear()
axarr[3].plot(args.epoch_assess_cluster_loss)
axarr[3].set_title("Cluster distance (assess, gt_k)")
distr_ax[0].clear()
epoch_distribution = np.array(args.epoch_distribution)
for gt_c in xrange(args.gt_k):
distr_ax[0].plot(epoch_distribution[:, gt_c])
distr_ax[0].set_title("Prediction distribution")
distr_ax[1].clear()
distr_ax[1].plot(args.epoch_centroid_min)
distr_ax[1].set_title("Centroid avg-of-abs: min")
distr_ax[2].clear()
distr_ax[2].plot(args.epoch_centroid_max)
distr_ax[2].set_title("Centroid avg-of-abs: max")
# save -----------------------------------------------------------------
# graphs
fig.canvas.draw_idle()
fig.savefig(os.path.join(args.out_dir, "plots.png"))
distr_fig.canvas.draw_idle()
distr_fig.savefig(os.path.join(args.out_dir, "distribution.png"))
# model
if epoch % args.checkpoint_granularity == 0:
torch.save({'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()},
os.path.join(args.out_dir, "latest.pytorch"))
args.epoch = epoch # last saved checkpoint
if is_best:
torch.save({'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()},
os.path.join(args.out_dir, "best.pytorch"))
args.best_epoch = epoch
# args
with open(os.path.join(args.out_dir, "config.pickle"), 'w') as outfile:
pickle.dump(args, outfile)
with open(os.path.join(args.out_dir, "config.txt"), "w") as text_file:
text_file.write("%s" % args)
for epoch in range(epochs):
end = time.time()
# remove head
model.top_layer_class = None
model.classifier = nn.Sequential(*list(model.classifier.children())[:-1])
###########################################################################
# if apply semi-supervised learning => stage1: unsupervised part
features_unlabel = compute_features(unlabel_loader,
model,
len(unlabel_dataset),
dataset_type='non-supervised')
clustering_loss_unlabel = deepcluster.cluster(features_unlabel,
verbose=verbose)
cluster_training_dataset = clustering.cluster_assign(
deepcluster.images_lists,
unlabel_dataset.imgs,
dataset_type='non-supervised')
unlabel_sampler = UnifLabelSampler(
int(reassign * len(cluster_training_dataset)),
deepcluster.images_lists)
cluster_dataloader = torch.utils.data.DataLoader(cluster_training_dataset,
batch_size=batch_size * C,
num_workers=12,
sampler=unlabel_sampler,
pin_memory=True)
mlp = list(model.classifier.children())
mlp.append(nn.ReLU(inplace=True).cuda())
model.classifier = nn.Sequential(*mlp)
model.top_layer_class = nn.Linear(fd, len(deepcluster.images_lists))
model.top_layer_class.weight.data.normal_(0, 0.01)
model.top_layer_class.bias.data.zero_()
