def main():
opt = parser.parse_args()
print(opt)
cuda = opt.cuda
if cuda:
print("=> use gpu id: '{}'".format(opt.gpus))
os.environ["CUDA_VISIBLE_DEVICES"] = str(opt.gpus)
if not torch.cuda.is_available():
raise Exception(
"No GPU found or Wrong GPU id, please run without --cuda")
print("===> Loading datasets")
dataset = BasicDataset(dir_img,
dir_mask,
transform=transforms.Compose([
transforms.ToTensor(),
transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
]))
training_data_loader = DataLoader(dataset=dataset, num_workers=opt.threads, \
batch_size=opt.batchSize, shuffle=True)
if opt.vgg_loss:
print("===> Loading VGG model")
netVGG = models.vgg19()
netVGG.load_state_dict(
model_zoo.load_url(
'https://download.pytorch.org/models/vgg19-dcbb9e9d.pth'))
class _content_model(nn.Module):
def __init__(self):
super(_content_model, self).__init__()
self.feature = nn.Sequential(
*list(netVGG.features.children())[:-1])
def forward(self, x):
out = self.feature(x)
return out
netContent = _content_model()
print("===> Building model")
model = NetG()
criterion = nn.MSELoss()
print("===> Setting Optimizer")
optimizer = optim.Adam(model.parameters(), lr=opt.lr)
print("===> Training")
for epoch in range(opt.start_epoch, opt.nEpochs + 1):
try:
os.makedirs('Output/{}'.format(epoch))
except Exception as e:
print(e)
train(training_data_loader, optimizer, model, criterion, epoch, opt,
netContent)
def __init__(self, model: nn.Module, checkpoint, image_net, random_samples,
indices, images_dir, use_cpu, name, image_resize, **kwargs):
self.checkpoint = checkpoint
self.image_net = image_net
self.random_samples = random_samples
self.indices = indices
self.image_resize = image_resize
self.device = common.get_device(cpu_force=use_cpu)
self.model = model
self.images_dir = images_dir
self.use_cpu = use_cpu
self.name = name
ch = get_checkpoint(checkpoint, image_net)
if ch is not None:
model.load_state_dict(ch, strict=False)
else:
print('Using random weights!')
self.dataset = BasicDataset(labels_csv=dataset_path(
prop('datasets.test')),
transforms=self.get_image_transforms(),
img_dir=self.images_dir)
self.mask_loader = MaskLoader(preset_attr=self.dataset.labels(),
ts=self.get_image_transforms())
self.label_to_index_total = {}
for i, name in enumerate(self.dataset.labels()):
self.label_to_index_total[name] = i
if self.random_samples is None and self.indices is None:
raise AttributeError(
'Expected one of `indices` or `random_samples`')
if self.indices is None and self.random_samples is not None:
self.indices = np.random.random_integers(low=0,
high=len(self.dataset) -
1,
size=self.random_samples)
def segment_img(img_path, net, device, scale_factor=1, out_threshold=0.5):
"""
Segement out the mask (target vein region) of the input image (specified by image path)
"""
print(f"\nPerforming segmentation on ---> {img_path} ...")
img = torch.from_numpy(BasicDataset.preprocess(Image.open(img_path).convert('L'), scale_factor))
img = img.unsqueeze(0) # add dimension
img = img.to(device=device, dtype=torch.float32)
begin_time = time.time()
with torch.no_grad():
output = net(img)
end_time = time.time()
inference_time = end_time - begin_time
print(f'inference_time: {inference_time}s')
# transform to image numpy array
if net.n_classes > 1:
probs = F.softmax(output, dim=1)
else:
probs = torch.sigmoid(output)
probs = probs.squeeze(0) #cuda tensor
tf = transforms.Compose(
[
transforms.ToPILImage(),
# transforms.Resize(full_img.size[1]),
transforms.ToTensor()
]
)
probs = tf(probs.cpu())
full_mask = probs.squeeze().cpu().numpy()
if np.count_nonzero(full_mask) == 0:
print("No veins segmented out on this image!")
return full_mask > out_threshold, inference_time
from dataset import BasicDataset
from torch.utils.data import DataLoader, random_split
from dynamic_dataloader import RestrictedDataset, BasicDataset
from fetch_data_for_next_phase import get_pool_data
# ailab
dir_img = '/data.local/all/hangd/src_code_3/Pytorch-UNet/data/imgs/'
dir_mask = '/data.local/all/hangd/src_code_3/Pytorch-UNet/data/masks/'
dir_img_test = '/data.local/all/hangd/src_code_3/Pytorch-UNet/data_test/imgs/'
dir_mask_test = '/data.local/all/hangd/src_code_3/Pytorch-UNet/data_test/masks/'
dir_img_draft = '/DATA/hangd/cardi/RobustSegmentation/data_draft/imgs/'
dir_mask_draft = '/DATA/hangd/cardi/RobustSegmentation/data_draft/masks/'
pool_data = get_pool_data("data_one32nd_category.json")
# dataset = RestrictedDataset(dir_img, dir_mask, pool_data, True)
dataset = BasicDataset(dir_img, dir_mask, pool_data)
pool_loader = DataLoader(dataset,
batch_size=16,
shuffle=True,
num_workers=1,
pin_memory=True)
batch = next(iter(pool_loader))
img = batch['image']
mask = batch['mask']
id = batch['id']
print("train_loader: ", img.shape, mask.shape)
print("id: ", id)
# GPU 사용 가능일 경우 랜덤 시드 고정
if device == 'cuda':
torch.cuda.manual_seed_all(777)
learning_rate = 1e-4
training_epochs = 500
batch_size = 10
os.chdir('C:/Users/CSD/Desktop/CPR_project/cnn')
from dataset import BasicDataset
os.chdir('C:/Users/CSD/Desktop/CPR_project/cnn')
mitdb_train = BasicDataset(root_dir='./data_mV', train=True)
data_loader = torch.utils.data.DataLoader(dataset=mitdb_train,
batch_size=batch_size,
shuffle=True,
drop_last=True)
mitdb_test = BasicDataset(root_dir='./data_mV', train=False)
data_loader_test = torch.utils.data.DataLoader(dataset=mitdb_test,
batch_size=batch_size,
shuffle=True,
drop_last=True)
class CNN(nn.Module):
def __init__(self):
super(CNN, self).__init__()
self.layer = nn.Sequential(
nn.Conv1d(1, 3, 5),
from dataset import BasicDataset
from torch.utils.data import DataLoader, random_split
dir_img = r"D:\BaiduNetdiskDownload\gen_img"
dir_mask = r"D:\BaiduNetdiskDownload\gen_mask"
dir_checkpoint = r"D:\PycharmsProjects\UNET+BLR\checkPoints"
classes = 5
epochs = 5
global_step = 0
batch_size = 4
lr = 0.001
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
dataset = BasicDataset(dir_img, dir_mask)
n_val = int(len(dataset) * 0.1)
n_train = len(dataset) - n_val
train, val = random_split(dataset, [n_train, n_val])
train_loader = DataLoader(train, batch_size=batch_size, shuffle=True)
val_loader = DataLoader(val, batch_size=batch_size, shuffle=False)
# writer = SummaryWriter(comment=f'LR_{lr}_BS_{batch_size}_SCALE_{1}')
net = UNet(n_channels=3, n_classes=classes, bilinear=True)
net = net.cuda()
optimizer = optim.Adam(net.parameters(), lr=lr, weight_decay=1e-8)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer, 'min' if net.n_classes > 1 else 'max', patience=2)
return [image, mask]
# use same transform for train/val for this example
trans = transforms.Compose(
[transforms.Resize((768, 768)),
transforms.ToTensor()])
# train_set = SimDataset(2000, transform=trans)
# val_set = SimDataset(200, transform=trans)
dir_img = 'data/imgs/'
dir_mask = 'data/masks/'
dataset = BasicDataset(dir_img, dir_mask, trans, scale=0.5)
val_percent = 0.1
n_val = int(len(dataset) * val_percent)
n_train = len(dataset) - n_val
train_set, val_set = random_split(dataset, [n_train, n_val])
batch_size = 1
image_datasets = {'train': train_set, 'val': val_set}
dataloaders = {
'train':
DataLoader(train_set, batch_size=batch_size, shuffle=True, num_workers=0),
'val':
DataLoader(val_set, batch_size=batch_size, shuffle=True, num_workers=0)
}
def train_net(
args,
net,
device,
epochs=5,
batch_size=1,
lr=0.1,
val_percent=0.1,
save_cp=True,
img_scale=0.5,
n_classes=2,
class_weights=[1, 1],
):
dataset = BasicDataset(dir_img, dir_mask, img_scale, n_classes)
n_val = int(len(dataset) * val_percent)
n_train = len(dataset) - n_val
train, val = random_split(dataset, [n_train, n_val])
train_loader = DataLoader(train,
batch_size=batch_size,
shuffle=True,
num_workers=8,
pin_memory=True)
val_loader = DataLoader(val,
batch_size=batch_size,
shuffle=False,
num_workers=8,
pin_memory=True)
writer = SummaryWriter(
comment=f'LR_{lr}_BS_{batch_size}_SCALE_{img_scale}')
global_step = 0
logging.info(f'''Starting training:
Epochs: {epochs}
Batch size: {batch_size}
Learning rate: {lr}
Training size: {n_train}
Validation size: {n_val}
Checkpoints: {save_cp}
Device: {device.type}
Images scaling: {img_scale}
''')
args.training_size = n_train
args.validation_size = n_val
argparse_dict = vars(args)
with open('./runs/config.list', 'w') as f:
f.write(json.dumps(argparse_dict, indent=4, sort_keys=True))
# optimizer = optim.RMSprop(net.parameters(), lr=lr, weight_decay=1e-8)
optimizer = optim.Adam(net.parameters(), lr=lr)
if net.n_classes > 1:
criterion = nn.CrossEntropyLoss(weight=torch.Tensor(class_weights).to(
device=device))
else:
criterion = nn.BCEWithLogitsLoss()
if os.path.exists('./runs/log.csv'):
os.remove('./runs/log.csv')
f = open('./runs/log.csv', 'a')
for epoch in range(epochs):
net.train()
epoch_loss = 0
with tqdm(total=n_train,
desc=f'Epoch {epoch + 1}/{epochs}',
unit='img') as pbar:
for batch in train_loader:
imgs = batch['image']
true_masks = batch['mask']
assert imgs.shape[1] == net.n_channels, \
f'Network has been defined with {net.n_channels} input channels, ' \
f'but loaded images have {imgs.shape[1]} channels. Please check that ' \
'the images are loaded correctly.'
imgs = imgs.to(device=device, dtype=torch.float32)
mask_type = torch.float32 if net.n_classes == 1 else torch.long
true_masks = true_masks.to(device=device, dtype=mask_type)
masks_pred = net(imgs)
loss = criterion(masks_pred, true_masks)
epoch_loss += loss.item()
writer.add_scalar('Loss/train', loss.item(), global_step)
pbar.set_postfix(**{'loss (batch)': loss.item()})
optimizer.zero_grad()
loss.backward()
optimizer.step()
tot = 0.
for true_mask, pred in zip(true_masks, masks_pred):
pred = (pred > 0.5).float()
tot += dice_coeff(pred, true_mask.squeeze(dim=1)).item()
acc = tot / len(imgs)
writer.add_scalar('Acc/train', acc, global_step)
log = [epoch] + [loss.item()] + [acc] + [' ']
log = map(str, log)
f.write(','.join(log) + '\n')
pbar.update(imgs.shape[0])
global_step += 1
if global_step % (len(dataset) // (10 * batch_size)) == 0:
val_score = eval_net(net, val_loader, device, n_val)
if net.n_classes > 1:
logging.info(
'Validation cross entropy: {}'.format(val_score))
writer.add_scalar('Loss/val', val_score, global_step)
else:
logging.info(
'Validation Dice Coeff: {}'.format(val_score))
writer.add_scalar('Acc/val', val_score, global_step)
writer.add_images('images', imgs, global_step)
if net.n_classes == 1:
writer.add_images('masks/true', true_masks,
global_step)
writer.add_images('masks/pred',
torch.sigmoid(masks_pred) > 0.5,
global_step)
log = [epoch] + [' '] + [' '] + [val_score]
log = map(str, log)
f.write(','.join(log) + '\n')
net.train()
if save_cp:
try:
os.mkdir(dir_checkpoint)
logging.info('Created checkpoint directory')
except OSError:
pass
torch.save(net.state_dict(),
dir_checkpoint + f'CP_epoch{epoch + 1}.pth')
logging.info(f'Checkpoint {epoch + 1} saved !')
writer.close()
def get_data_statistics(data_path,
model,
dims=DIMS,
cuda=True,
batch_size=BATCH_SIZE):
# Create temporary dump directory
tag = get_tag(data_path, dims)
fname = os.path.join(STATISTICS_DIR, tag + '.npz')
# Check if statistics exist
if os.path.exists(fname):
stats = np.load(fname)
m, s, num = stats['m'], stats['s'], stats['num_samples']
else:
temp_path = os.path.join(TEMP_DIR, tag) + '/'
if not os.path.exists(temp_path):
os.mkdir(temp_path)
# Load all images and convert to save as 0-255 .png or .jpg (normalize per image)
dataset = BasicDataset(model_dir=data_path)
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=batch_size,
num_workers=4,
shuffle=False)
num = 0
for batch in dataloader:
batch = batch.detach().cpu().numpy()
batch = ((batch + 1) / 2 * 255).astype(np.uint8)
for i in range(batch.shape[0]):
img = np.tile(batch[i].transpose(1, 2, 0), (1, 1, 3))
imsave(os.path.join(temp_path, f'img_{num}.png'), img)
num += 1
else:
num = len(os.listdir(temp_path))
if cuda:
model.cuda()
m, s = fid_score._compute_statistics_of_path(temp_path,
model,
batch_size=batch_size,
cuda=cuda,
dims=dims)
# Remove dump folder
rmtree(temp_path)
np.savez(fname, m=m, s=s, num_samples=num)
return m, s, num
net = UNet(n_channels=1, n_classes=1).to(
device) # we are using gray images and only have one labelled class
if args.pretrained_weights:
net.load_state_dict(torch.load(args.pretrained_weights))
print(f'Pretrained weights loaded from {args.load}')
print(
f' Using device {device}\n Network:\n \t{net.n_channels} input channels\n \t{net.n_classes} output channels (classes)\n \t{"Bilinear" if net.bilinear else "Dilated conv"} upscaling'
)
# faster convolutions, but more memory
# cudnn.benchmark = True
## --- Set up data
imgs_dir = 'data/imgs/' + args.dataset_name
masks_dir = 'data/masks/' + args.dataset_name
print(f'imgs_dir: {imgs_dir} masks_dir: {masks_dir}')
dataset = BasicDataset(imgs_dir, masks_dir, args.down_scale)
n_val = int(len(dataset) * args.valid_ratio)
n_train = len(dataset) - n_val
print(f'n_val: {n_val} n_train: {n_train}')
train, val = random_split(
dataset,
[n_train, n_val]) #split into train dataset and validation dataset
train_loader = DataLoader(train,
batch_size=args.batch_size,
shuffle=True,
num_workers=1,
pin_memory=True)
val_loader = DataLoader(val,
batch_size=args.batch_size,
shuffle=False,
num_workers=1,
net = ClassifierModule10_2path(backbone10=args.backbone_10, backbone3=args.backbone_10, fcnn=False)
if args.setup == 'two_path_fcnn':
net = ClassifierModule10_2path(backbone10=args.backbone_10, backbone3=args.backbone_10, fcnn=True)
if args.setup == 'single_path':
net = ClassifierModule10(backbone=args.backbone_10)
# net = BaseLine()
net.to(device=device)
weigths = torch.load(args.weights, map_location=device)
if args.n_classes == 3:
weigths, total_size_new = quantize_weights(weigths, 4)
# weigths = pruning(weigths, 0.009, total_size_new)
net.load_state_dict(weigths)
# torch.quantization.quantize_dynamic(
# net, # the original model
# {torch.nn.Linear}, # a set of layers to dynamically quantize
# dtype=torch.qint8) # the target dtype for quantized weights
net.eval()
# test data loader
dataset_test = BasicDataset(args.data_dir, args.features_dir, test_df, args.n_classes, test=True,
augmentations='without')
test_loader = DataLoader(dataset_test, batch_size=args.batch_size, shuffle=False, num_workers=8, pin_memory=True,
drop_last=False)
prediction, labels = get_prediction(test_loader, net, device, args.setup)
plot_results(prediction, labels, args.output_dir, rec_device='all', n_classes=args.n_classes)
rec_devices = test_df.apply(lambda x: x['filename'].split('/')[1].split('-')[-1].replace('.wav', ''), axis=1)
for rec_device in rec_devices.unique():
prediction_partial = prediction[rec_devices == rec_device]
labels_partial = labels[rec_devices == rec_device]
plot_results(prediction_partial, labels_partial, args.output_dir, rec_device=rec_device,
n_classes=args.n_classes)
class BaseTestModel:
def __init__(self, model: nn.Module, checkpoint, image_net, random_samples,
indices, images_dir, use_cpu, name, image_resize, **kwargs):
self.checkpoint = checkpoint
self.image_net = image_net
self.random_samples = random_samples
self.indices = indices
self.image_resize = image_resize
self.device = common.get_device(cpu_force=use_cpu)
self.model = model
self.images_dir = images_dir
self.use_cpu = use_cpu
self.name = name
ch = get_checkpoint(checkpoint, image_net)
if ch is not None:
model.load_state_dict(ch, strict=False)
else:
print('Using random weights!')
self.dataset = BasicDataset(labels_csv=dataset_path(
prop('datasets.test')),
transforms=self.get_image_transforms(),
img_dir=self.images_dir)
self.mask_loader = MaskLoader(preset_attr=self.dataset.labels(),
ts=self.get_image_transforms())
self.label_to_index_total = {}
for i, name in enumerate(self.dataset.labels()):
self.label_to_index_total[name] = i
if self.random_samples is None and self.indices is None:
raise AttributeError(
'Expected one of `indices` or `random_samples`')
if self.indices is None and self.random_samples is not None:
self.indices = np.random.random_integers(low=0,
high=len(self.dataset) -
1,
size=self.random_samples)
def get_image_transforms(self):
return transforms.Compose([
transforms.Resize((self.image_resize, self.image_resize),
interpolation=Image.NEAREST),
transforms.ToTensor()
])
def process_one(self, image, target, model_output_all, masks, image_index,
in_batch_index):
raise NotImplementedError
def run(self):
self.model = self.model.to(self.device)
self.model.eval()
images_batch, target_batch, img_indices_batch = batch_by_indices(
ds=self.dataset, indices=self.indices)
masks = self.mask_loader[img_indices_batch]
model_out = self.model(images_batch.to(self.device))
for i, image_index in enumerate(img_indices_batch):
self.process_one(image=images_batch[i],
target=target_batch[i],
model_output_all=model_out,
masks=masks[i],
image_index=image_index,
in_batch_index=i)
def train_net(dir_checkpoint,
n_classes,
bilinear,
n_channels,
device,
epochs=30,
val_percent=0.1,
save_cp=True,
img_scale=1):
global best_val_iou_score
global best_test_iou_score
net = PAN()
# net = smp.Unet(
# encoder_name='timm-regnety_120', # choose encoder, e.g. mobilenet_v2 or efficientnet-b7
# encoder_weights=None, # use `imagenet` pretrained weights for encoder initialization
# in_channels=3, # model input channels (1 for grayscale images, 3 for RGB, etc.)
# classes=1, # model output channels (number of classes in your dataset)
# )
net.to(device=device)
dataset = BasicDataset(dir_img, dir_mask, img_scale)
data_test = BasicDataset(imgs_dir=dir_img_test,
masks_dir=dir_mask_test,
train=False,
scale=img_scale)
batch_size = 4
train_loader = DataLoader(dataset,
batch_size=batch_size,
shuffle=True,
num_workers=4,
pin_memory=True)
test_loader = DataLoader(data_test,
batch_size=batch_size,
shuffle=False,
num_workers=2,
pin_memory=True,
drop_last=True)
lr = 1e-5
writer = SummaryWriter(
comment=
f'_{net.__class__.__name__}_LR_{lr}_BS_{batch_size}_SCALE_{img_scale}')
global_step = 0
logging.info(f'''Starting training:
Epochs: {epochs}
Batch size: {batch_size}
Learning rate: {lr}
Checkpoints: {save_cp}
Device: {device.type}
Images scaling: {img_scale}
''')
optimizer = optim.RMSprop(net.parameters(),
lr=lr,
weight_decay=1e-8,
momentum=0.9)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer, 'min' if n_classes > 1 else 'max', patience=2)
if n_classes > 1:
criterion = nn.CrossEntropyLoss()
else:
criterion = nn.BCEWithLogitsLoss()
for epoch in range(epochs):
net.train()
epoch_loss = 0
n_train = len(dataset)
with tqdm(total=n_train,
desc=f'Epoch {epoch + 1}/{epochs}',
unit='img') as pbar:
for batch in train_loader:
imgs = batch['image']
true_masks = batch['mask']
assert imgs.shape[1] == n_channels, \
f'Network has been defined with {n_channels} input channels, ' \
f'but loaded images have {imgs.shape[1]} channels. Please check that ' \
'the images are loaded correctly.'
imgs = imgs.to(device=device, dtype=torch.float32)
mask_type = torch.float32 if n_classes == 1 else torch.long
true_masks = true_masks.to(device=device, dtype=mask_type)
masks_pred = net(imgs) # return BCHW = 8_1_256_256
_tem = net(imgs)
# print("IS DIFFERENT OR NOT: ", torch.sum(masks_pred - _tem))
true_masks = true_masks[:, :1, :, :]
loss = criterion(masks_pred, true_masks)
epoch_loss += loss.item()
# writer.add_scalar('Loss/train', loss.item(), global_step)
pbar.set_postfix(**{'loss (batch)': loss.item()})
optimizer.zero_grad()
loss.backward()
nn.utils.clip_grad_value_(net.parameters(), 0.1)
optimizer.step()
pbar.update(imgs.shape[0])
global_step += 1
# Tính dice và iou score trên tập Test set, ghi vào tensorboard .
test_score_dice, test_score_iou = eval_net(net, test_loader, n_classes,
device)
if test_score_iou > best_test_iou_score:
best_test_iou_score = test_score_iou
try:
os.mkdir(dir_checkpoint)
logging.info('Created checkpoint directory')
except OSError:
pass
torch.save(net.state_dict(),
dir_checkpoint + f'best_CP_epoch{epoch + 1}.pth')
logging.info(f'Checkpoint {epoch + 1} saved !')
logging.info('Test Dice Coeff: {}'.format(test_score_dice))
print('Test Dice Coeff: {}'.format(test_score_dice))
writer.add_scalar('Dice/test', test_score_dice, epoch)
logging.info('Test IOU : {}'.format(test_score_iou))
print('Test IOU : {}'.format(test_score_iou))
writer.add_scalar('IOU/test', test_score_iou, epoch)
print("best iou: ", best_test_iou_score)
def train_net(dir_checkpoint,
n_classes,
bilinear,
n_channels,
device,
epochs=30,
val_percent=0.1,
save_cp=True,
img_scale=1):
global best_val_iou_score
global best_test_iou_score
net = PAN()
ckpt_path = "/data.local/all/hangd/v1/uncertainty1/best_CP_epoch29_one32th_.pth"
net.to(device=device)
net.load_state_dict(torch.load(ckpt_path, map_location=device))
writer = SummaryWriter(
comment=f'_{net.__class__.__name__}_ece_one32nd_training_set')
logging.info(f'Model loaded from {ckpt_path}')
batch_size = 4
dataset = BasicDataset(dir_img, dir_mask, True)
pool_loader = DataLoader(dataset,
batch_size=batch_size,
shuffle=True,
num_workers=4,
pin_memory=True)
# data_test = BasicDataset(imgs_dir=dir_img_test, masks_dir=dir_mask_test, train=False, scale=img_scale)
# test_loader = DataLoader(data_test, batch_size=16, shuffle=False, num_workers=2, pin_memory=True,drop_last=True)
logging.info(f'''Starting selecting in pool:
Device: {device.type}
''')
epochs = 1
# test_score_dice, test_score_iou = eval_net(net, test_loader, n_classes, device)
# print(f"TEST iou = {test_score_iou}, dice = {test_score_dice} ")
std = []
for epoch in range(epochs):
net.eval()
epoch_loss = 0
n_pool = len(dataset)
with tqdm(total=n_pool,
desc='ECE calculating',
unit='batch',
leave=False) as pbar:
for ind, batch in enumerate(tqdm(pool_loader)):
imgs, true_masks = batch['image'], batch['mask']
imgs = imgs.to(device=device, dtype=torch.float32)
true_masks = true_masks.to(device=device,
dtype=torch.float32) # BHWC
true_masks = true_masks[:, :1, :, :]
y_pred_samples = []
for i in range(GAUSS_ITERATION):
with torch.no_grad():
logits = net(imgs)
y_pred = torch.sigmoid(logits)
# y_pred = (y_pred > 0.5).float()
y_pred = y_pred[:, :1, :, :]
y_pred_samples.append(
y_pred[:, 0, :, :]
) # y_pred_samples's shape: (inx, bat, H, W )
y_pred_samples = torch.stack(y_pred_samples, dim=0)
y_pred_samples = y_pred_samples.type(torch.FloatTensor)
mean_y_pred = y_pred_samples.mean(dim=0) # shape: batch, H, W
std_y_pred = y_pred_samples.std(dim=0) # shape: batch, H, W
grid = torchvision.utils.make_grid(mean_y_pred.unsqueeze(1))
writer.add_image('images', grid, ind)
_std = get_segmentation_mask_uncertainty(std_y_pred)
std.extend(_std)
for ind, val in enumerate(std):
writer.add_scalar("std in pool - case one32nd data", val, ind)
writer.add_histogram("Histogram std corresponding", np.array(std), 1)
std = torch.cuda.FloatTensor(std)
mean = std.mean()
_std = std.std()
writer.add_scalar("Mean std", mean, 1)
writer.add_scalar("STD std", _std, 1)
print("Mean: ", mean)
print("std: ", _std)
def train_net(dir_checkpoint,
n_classes,
bilinear,
n_channels,
device,
epochs=30,
val_percent=0.1,
save_cp=True,
img_scale=1):
global best_val_iou_score
global best_test_iou_score
net = PAN()
ckpt_path = "/data.local/all/hangd/v1/uncertainty1/best_CP_epoch15_test_iou_85_with_25_percent_original_training_dataset.pth"
net.to(device=device)
net.load_state_dict(torch.load(ckpt_path, map_location=device))
logging.info(f'Model loaded from {ckpt_path}')
dataset = BasicDataset(dir_img, dir_mask, img_scale)
data_test = BasicDataset(imgs_dir=dir_img_test,
masks_dir=dir_mask_test,
train=False,
scale=img_scale)
batch_size = 4
train_loader = DataLoader(dataset,
batch_size=batch_size,
shuffle=True,
num_workers=4,
pin_memory=True)
lr = 1e-5
writer = SummaryWriter(
comment=f'_{net.__class__.__name__}_ECE_on_25percentage_data')
global_step = 0
logging.info(f'''Starting training:
Device: {device.type}
''')
epochs = 1
ece_values = []
for epoch in range(epochs):
net.train()
epoch_loss = 0
n_train = len(dataset)
with tqdm(total=n_train,
desc='Validation round',
unit='batch',
leave=False) as pbar:
for batch in train_loader:
imgs, true_masks = batch['image'], batch['mask']
imgs = imgs.to(device=device, dtype=torch.float32)
true_masks = true_masks.to(device=device,
dtype=torch.float32) # BHWC
true_masks = true_masks[:, :1, :, :]
y_pred_samples = []
for i in range(GAUSS_ITERATION):
with torch.no_grad():
logits = net(imgs)
y_pred = torch.sigmoid(logits)
# y_pred = (y_pred > 0.5).float()
y_pred = y_pred[:, :1, :, :]
y_pred_samples.append(
y_pred[:, 0, :, :]
) # y_pred_samples's shape: (inx, bat, H, W )
y_pred_samples = torch.stack(y_pred_samples, dim=0)
y_pred_samples = y_pred_samples.type(torch.FloatTensor)
mean_y_pred = y_pred_samples.mean(dim=0) # shape: batch, H, W
ece_values.extend(
get_segmentation_mask_uncertainty(mean_y_pred, true_masks))
pbar.update()
for inx, ece_val in enumerate(ece_values):
writer.add_scalar("ECE_on_quarter_of_training_set", ece_val, inx)
def train_net(dir_checkpoint,
n_classes,
n_channels,
device,
epochs=30,
save_cp=True,
img_scale=1):
global best_val_iou_score
global best_test_iou_score
net = PAN()
net.to(device=device)
batch_size = 4
lr = 1e-5
writer = SummaryWriter(
comment=
f'_{net.__class__.__name__}_LR_{lr}_BS_{batch_size}_categoryFirstEntropy_ACQUISITION'
)
global_step = 0
logging.basicConfig(
filename="./logging_one32nd_category.txt",
filemode='a',
format='%(asctime)s,%(msecs)d %(name)s %(levelname)s %(message)s',
datefmt='%Y-%m-%d %H:%M:%S',
level=logging.DEBUG)
logging.info(f'''Starting training:
Epochs: {epochs}
Batch size: {batch_size}
Learning rate: {lr}
Checkpoints: {save_cp}
Device: {device.type}
''')
optimizer = optim.RMSprop(net.parameters(),
lr=lr,
weight_decay=1e-8,
momentum=0.9)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer, 'min' if n_classes > 1 else 'max', patience=2)
if n_classes > 1:
criterion = nn.CrossEntropyLoss()
else:
criterion = nn.BCEWithLogitsLoss()
num_phases = 25 # total 2689 imgs, within each phase: fetching 100 imgs to training set.
training_pool_ids_path = "data_one32nd_category.json"
all_training_data = "data_all.json"
for phase in range(num_phases):
# Within a phase, save the best epoch (having highest test_iou) checkpoint and save its test_iou to TF_Board
# also, load the best right previous checkpoint
selected_images = get_pool_data(training_pool_ids_path)
data_train = RestrictedDataset(dir_img, dir_mask, selected_images)
data_test = BasicDataset(imgs_dir=dir_img_test,
masks_dir=dir_mask_test,
train=False,
scale=img_scale)
train_loader = DataLoader(data_train,
batch_size=batch_size,
shuffle=True,
num_workers=4,
pin_memory=True)
test_loader = DataLoader(data_test,
batch_size=batch_size,
shuffle=False,
num_workers=2,
pin_memory=True,
drop_last=True)
right_previous_ckpt_dir = Path(dir_checkpoint + 'ckpt.pth')
if right_previous_ckpt_dir.is_file():
net.load_state_dict(
torch.load(dir_checkpoint + 'ckpt.pth', map_location=device))
for epoch in range(epochs):
net.train()
epoch_loss = 0
n_train = len(data_train)
with tqdm(total=n_train,
desc=f'Epoch {epoch + 1}/{epochs}',
unit='img') as pbar:
for batch in train_loader:
imgs = batch['image']
true_masks = batch['mask']
assert imgs.shape[1] == n_channels, \
f'Network has been defined with {n_channels} input channels, ' \
f'but loaded images have {imgs.shape[1]} channels. Please check that ' \
'the images are loaded correctly.'
imgs = imgs.to(device=device, dtype=torch.float32)
mask_type = torch.float32 if n_classes == 1 else torch.long
true_masks = true_masks.to(device=device, dtype=mask_type)
masks_pred = net(imgs) # return BCHW = 8_1_256_256
_tem = net(imgs)
# print("IS DIFFERENT OR NOT: ", torch.sum(masks_pred - _tem))
true_masks = true_masks[:, :1, :, :]
loss = criterion(masks_pred, true_masks)
epoch_loss += loss.item()
# writer.add_scalar('Loss/train', loss.item(), global_step)
pbar.set_postfix(**{'loss (batch)': loss.item()})
optimizer.zero_grad()
loss.backward()
nn.utils.clip_grad_value_(net.parameters(), 0.1)
optimizer.step()
pbar.update(imgs.shape[0])
global_step += 1
# Tính dice và iou score trên tập Test set, ghi vào tensorboard .
test_score_dice, test_score_iou = eval_net(net, test_loader,
n_classes, device)
if test_score_iou > best_test_iou_score:
best_test_iou_score = test_score_iou
try:
os.mkdir(dir_checkpoint)
logging.info('Created checkpoint directory')
except OSError:
pass
torch.save(
net.state_dict(),
dir_checkpoint + f'best_CP_epoch{epoch + 1}_one32th_.pth')
logging.info(f'Checkpoint {epoch + 1} saved !')
logging.info('Test Dice Coeff: {}'.format(test_score_dice))
print('Test Dice Coeff: {}'.format(test_score_dice))
writer.add_scalar(f'Phase_{phase}_Dice/test', test_score_dice,
epoch)
logging.info('Test IOU : {}'.format(test_score_iou))
print('Test IOU : {}'.format(test_score_iou))
writer.add_scalar(f'Phase_{phase}_IOU/test', test_score_iou, epoch)
print(f"Phase_{phase}_best iou: ", best_test_iou_score)
torch.save(net.state_dict(), dir_checkpoint + 'ckpt.pth')
writer.add_scalar('Phase_IOU/test', best_test_iou_score, phase)
# Fetching data for next phase - Update pooling images.
update_training_pool_ids_2(net,
training_pool_ids_path,
all_training_data,
device,
acquisition_func="cfe")
writer.close()
default='checkpoints/CP_epoch100.pth') # checkpoints/CP_epoch51.pth
logging.basicConfig(level=logging.INFO, format='%(levelname)s: %(message)s')
#using tensorboard: tensorboard --logdir=runs
if __name__ == "__main__":
opt = parser.parse_args()
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
net = UNet(n_channels=3, n_classes=2)
if opt.load_cp != '':
net.load_state_dict(torch.load(opt.load_cp, map_location=device))
net.to(device=device)
# faster convolutions, but more memory
# cudnn.benchmark = True
dataset = BasicDataset(opt.dir_patch)
n_val = int(len(dataset) * opt.val_percent)
n_train = len(dataset) - n_val
train, val = random_split(dataset, [n_train, n_val])
train_loader = DataLoader(train,
batch_size=opt.batch_size,
shuffle=True,
num_workers=int(opt.workers),
pin_memory=True)
val_loader = DataLoader(val,
batch_size=opt.batch_size,
shuffle=False,
num_workers=int(opt.workers),
pin_memory=True)
writer = SummaryWriter(
comment=f'_lr{opt.learning_rate}_bs{opt.batch_size}')
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 26 13:05:03 2020
@author: mooselumph
"""
import torch.utils.data
from dataset import BasicDataset
dataroot = 'C:/Users/mooselumph/code/data/velocity/'
dataset = BasicDataset(model_dir=dataroot)
dataloader = torch.utils.data.DataLoader(dataset,
batch_size=10,
shuffle=False,
num_workers=1)
for batch in dataloader:
print(batch.shape)
image_folder = args.image_folder + '/' + args.dataset_name
for i, fn in enumerate(os.listdir(image_folder)):
if not fn.endswith('.jpg'):
continue
count += 1
# input image
img_path = os.path.join(image_folder, fn)
target_path = img_path.replace('imgs', 'masks')
# single image prediction
mask, inference_time = segment_img(img_path, net, device, args.scale, args.mask_threshold)
# target mask
# FloatTensor = torch.cuda.FloatTensor if torch.cuda.is_available() else torch.FloatTensor
FloatTensor = torch.cuda.FloatTensor if args.device == 'cuda' else torch.FloatTensor
target = BasicDataset.preprocess(Image.open(target_path), args.scale)
# validation score computation
val_score = dice_coeff(FloatTensor(mask), FloatTensor(target).squeeze(0)).item()
print(f'validation_score (dice_coeff): {val_score}')
val_score_total += val_score
# prediction speed
inference_time_total += inference_time
if args.save_results:
output_path = os.path.join(output_dir, fn)
mask_to_image(mask).save(output_path)
print(f"saved predicted mask to ---> {output_path}")
if args.viz:
