def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'--model-file',
type=str,
default='./logs/train2/20181202_160326.365442/checkpoint_9.pth.tar',
help='Model path')
parser.add_argument('--dataset',
type=str,
default='Drishti-GS',
help='test folder id contain images ROIs to test')
parser.add_argument('-g', '--gpu', type=int, default=0)
parser.add_argument('--data-dir',
default='/home/sjwang/ssd1T/fundus/domain_adaptation/',
help='data root path')
parser.add_argument(
'--out-stride',
type=int,
default=16,
help='out-stride of deeplabv3+',
)
parser.add_argument(
'--save-root-ent',
type=str,
default='./results/ent/',
help='path to save ent',
)
parser.add_argument(
'--save-root-mask',
type=str,
default='./results/mask/',
help='path to save mask',
)
parser.add_argument(
'--sync-bn',
type=bool,
default=True,
help='sync-bn in deeplabv3+',
)
parser.add_argument(
'--freeze-bn',
type=bool,
default=False,
help='freeze batch normalization of deeplabv3+',
)
parser.add_argument('--test-prediction-save-path',
type=str,
default='./results/baseline/',
help='Path root for test image and mask')
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
model_file = args.model_file
# 1. dataset
composed_transforms_test = transforms.Compose(
[tr.Normalize_tf(), tr.ToTensor()])
db_test = DL.FundusSegmentation(base_dir=args.data_dir,
dataset=args.dataset,
split='test',
transform=composed_transforms_test)
test_loader = DataLoader(db_test,
batch_size=1,
shuffle=False,
num_workers=1)
# 2. model
model = DeepLab(num_classes=2,
backbone='mobilenet',
output_stride=args.out_stride,
sync_bn=args.sync_bn,
freeze_bn=args.freeze_bn).cuda()
if torch.cuda.is_available():
model = model.cuda()
print('==> Loading %s model file: %s' %
(model.__class__.__name__, model_file))
checkpoint = torch.load(model_file)
try:
model.load_state_dict(model_data)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model_gen.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {
k: v
for k, v in pretrained_dict.items() if k in model_dict
}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model_gen.load_state_dict(model_dict)
except Exception:
model.load_state_dict(checkpoint['model_state_dict'])
model.eval()
print('==> Evaluating with %s' % (args.dataset))
val_cup_dice = 0.0
val_disc_dice = 0.0
timestamp_start = \
datetime.now(pytz.timezone('Asia/Hong_Kong'))
for batch_idx, (sample) in tqdm.tqdm(enumerate(test_loader),
total=len(test_loader),
ncols=80,
leave=False):
data = sample['image']
target = sample['map']
img_name = sample['img_name']
if torch.cuda.is_available():
data, target = data.cuda(), target.cuda()
data, target = Variable(data), Variable(target)
prediction, boundary = model(data)
prediction = torch.nn.functional.interpolate(prediction,
size=(target.size()[2],
target.size()[3]),
mode="bilinear")
boundary = torch.nn.functional.interpolate(boundary,
size=(target.size()[2],
target.size()[3]),
mode="bilinear")
data = torch.nn.functional.interpolate(data,
size=(target.size()[2],
target.size()[3]),
mode="bilinear")
prediction = torch.sigmoid(prediction)
boundary = torch.sigmoid(boundary)
draw_ent(prediction.data.cpu()[0].numpy(),
os.path.join(args.save_root_ent, args.dataset), img_name[0])
draw_mask(prediction.data.cpu()[0].numpy(),
os.path.join(args.save_root_mask, args.dataset), img_name[0])
draw_boundary(boundary.data.cpu()[0].numpy(),
os.path.join(args.save_root_mask, args.dataset),
img_name[0])
prediction = postprocessing(prediction.data.cpu()[0],
dataset=args.dataset)
target_numpy = target.data.cpu()
cup_dice = dice_coefficient_numpy(prediction[0, ...],
target_numpy[0, 0, ...])
disc_dice = dice_coefficient_numpy(prediction[1, ...],
target_numpy[0, 1, ...])
val_cup_dice += cup_dice
val_disc_dice += disc_dice
imgs = data.data.cpu()
for img, lt, lp in zip(imgs, target_numpy, [prediction]):
img, lt = untransform(img, lt)
save_per_img(img.numpy().transpose(1, 2, 0),
os.path.join(args.test_prediction_save_path,
args.dataset),
img_name[0],
lp,
mask_path=None,
ext="bmp")
val_cup_dice /= len(test_loader)
val_disc_dice /= len(test_loader)
print('''\n==>val_cup_dice : {0}'''.format(val_cup_dice))
print('''\n==>val_disc_dice : {0}'''.format(val_disc_dice))
with open(osp.join(args.test_prediction_save_path, 'test_log.csv'),
'a') as f:
elapsed_time = (datetime.now(pytz.timezone('Asia/Hong_Kong')) -
timestamp_start).total_seconds()
log = [[args.model_file] + ['cup dice coefficence: '] + \
[val_cup_dice] + ['disc dice coefficence: '] + \
[val_disc_dice] + [elapsed_time]]
log = map(str, log)
f.write(','.join(log) + '\n')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--model-file', type=str, default='./logs/test1/20190506_221021.177567/checkpoint_200.pth.tar', help='Model path')
parser.add_argument('--datasetTest', type=list, default=[1], help='test folder id contain images ROIs to test')
parser.add_argument('--dataset', type=str, default='test', help='test folder id contain images ROIs to test')
parser.add_argument('-g', '--gpu', type=int, default=0)
parser.add_argument('--data-dir', default='../../../../Dataset/Fundus/', help='data root path')
parser.add_argument('--out-stride', type=int, default=16, help='out-stride of deeplabv3+',)
parser.add_argument('--sync-bn', type=bool, default=False, help='sync-bn in deeplabv3+')
parser.add_argument('--freeze-bn', type=bool, default=False, help='freeze batch normalization of deeplabv3+')
parser.add_argument('--movingbn', type=bool, default=False, help='moving batch normalization of deeplabv3+ in the test phase',)
parser.add_argument('--test-prediction-save-path', type=str, default='./results/rebuttle-0401/', help='Path root for test image and mask')
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
model_file = args.model_file
output_path = os.path.join(args.test_prediction_save_path, 'test' + str(args.datasetTest[0]), args.model_file.split('/')[-2])
# 1. dataset
composed_transforms_test = transforms.Compose([
tr.Normalize_tf(),
tr.ToTensor()
])
db_test = DL.FundusSegmentation(base_dir=args.data_dir, phase='test', splitid=args.datasetTest,
transform=composed_transforms_test, state='prediction')
batch_size = 12
test_loader = DataLoader(db_test, batch_size=batch_size, shuffle=False, num_workers=1)
# 2. model
model = DeepLab(num_classes=2, backbone='mobilenet', output_stride=args.out_stride,
sync_bn=args.sync_bn, freeze_bn=args.freeze_bn).cuda()
if torch.cuda.is_available():
model = model.cuda()
print('==> Loading %s model file: %s' %
(model.__class__.__name__, model_file))
# model_data = torch.load(model_file)
checkpoint = torch.load(model_file)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model.load_state_dict(model_dict)
if args.movingbn:
model.train()
else:
model.eval()
val_cup_dice = 0.0
val_disc_dice = 0.0
total_hd_OC = 0.0
total_hd_OD = 0.0
total_asd_OC = 0.0
total_asd_OD = 0.0
timestamp_start = datetime.now(pytz.timezone('Asia/Hong_Kong'))
total_num = 0
OC = []
OD = []
for batch_idx, (sample) in tqdm.tqdm(enumerate(test_loader),total=len(test_loader),ncols=80, leave=False):
data = sample['image']
target = sample['label']
img_name = sample['img_name']
if torch.cuda.is_available():
data, target = data.cuda(), target.cuda()
data, target = Variable(data), Variable(target)
prediction, dc, sel, _ = model(data)
prediction = torch.nn.functional.interpolate(prediction, size=(target.size()[2], target.size()[3]), mode="bilinear")
data = torch.nn.functional.interpolate(data, size=(target.size()[2], target.size()[3]), mode="bilinear")
target_numpy = target.data.cpu()
imgs = data.data.cpu()
hd_OC = 100
asd_OC = 100
hd_OD = 100
asd_OD = 100
for i in range(prediction.shape[0]):
prediction_post = postprocessing(prediction[i], dataset=args.dataset)
cup_dice, disc_dice = dice_coeff_2label(prediction_post, target[i])
OC.append(cup_dice)
OD.append(disc_dice)
if np.sum(prediction_post[0, ...]) < 1e-4:
hd_OC = 100
asd_OC = 100
else:
hd_OC = binary.hd95(np.asarray(prediction_post[0, ...], dtype=np.bool),
np.asarray(target_numpy[i, 0, ...], dtype=np.bool))
asd_OC = binary.asd(np.asarray(prediction_post[0, ...], dtype=np.bool),
np.asarray(target_numpy[i, 0, ...], dtype=np.bool))
if np.sum(prediction_post[0, ...]) < 1e-4:
hd_OD = 100
asd_OD = 100
else:
hd_OD = binary.hd95(np.asarray(prediction_post[1, ...], dtype=np.bool),
np.asarray(target_numpy[i, 1, ...], dtype=np.bool))
asd_OD = binary.asd(np.asarray(prediction_post[1, ...], dtype=np.bool),
np.asarray(target_numpy[i, 1, ...], dtype=np.bool))
val_cup_dice += cup_dice
val_disc_dice += disc_dice
total_hd_OC += hd_OC
total_hd_OD += hd_OD
total_asd_OC += asd_OC
total_asd_OD += asd_OD
total_num += 1
for img, lt, lp in zip([imgs[i]], [target_numpy[i]], [prediction_post]):
img, lt = utils.untransform(img, lt)
save_per_img(img.numpy().transpose(1, 2, 0),
output_path,
img_name[i],
lp, lt, mask_path=None, ext="bmp")
print('OC:', OC)
print('OD:', OD)
import csv
with open('Dice_results.csv', 'a+') as result_file:
wr = csv.writer(result_file, dialect='excel')
for index in range(len(OC)):
wr.writerow([OC[index], OD[index]])
val_cup_dice /= total_num
val_disc_dice /= total_num
total_hd_OC /= total_num
total_asd_OC /= total_num
total_hd_OD /= total_num
total_asd_OD /= total_num
print('''\n==>val_cup_dice : {0}'''.format(val_cup_dice))
print('''\n==>val_disc_dice : {0}'''.format(val_disc_dice))
print('''\n==>average_hd_OC : {0}'''.format(total_hd_OC))
print('''\n==>average_hd_OD : {0}'''.format(total_hd_OD))
print('''\n==>ave_asd_OC : {0}'''.format(total_asd_OC))
print('''\n==>average_asd_OD : {0}'''.format(total_asd_OD))
with open(osp.join(output_path, '../test' + str(args.datasetTest[0]) + '_log.csv'), 'a') as f:
elapsed_time = (
datetime.now(pytz.timezone('Asia/Hong_Kong')) -
timestamp_start).total_seconds()
log = [['batch-size: '] + [batch_size] + [args.model_file] + ['cup dice coefficence: '] + \
[val_cup_dice] + ['disc dice coefficence: '] + \
[val_disc_dice] + ['average_hd_OC: '] + \
[total_hd_OC] + ['average_hd_OD: '] + \
[total_hd_OD] + ['ave_asd_OC: '] + \
[total_asd_OC] + ['average_asd_OD: '] + \
[total_asd_OD] + [elapsed_time]]
log = map(str, log)
f.write(','.join(log) + '\n')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--model-file', type=str, default='./logs/refuge_weights.tar',
help='Model path')
parser.add_argument(
'--dataset', type=str, default='Drishti-GS', help='test folder id contain images ROIs to test'
)
parser.add_argument('-g', '--gpu', type=int, default=0)
parser.add_argument(
'--resize', type=int, default=800, help='image resize')
parser.add_argument(
'--data-dir',
default='./fundus/',
help='data root path'
)
parser.add_argument(
'--mask-dir',
required=True,
default='./fundus/Drishti-GS/test/mask',
help='mask image path'
)
parser.add_argument(
'--out-stride',
type=int,
default=16,
help='out-stride of deeplabv3+',
)
parser.add_argument(
'--save-root-ent',
type=str,
default='./results/ent/',
help='path to save ent',
)
parser.add_argument(
'--save-root-mask',
type=str,
default='./results/mask/',
help='path to save mask',
)
parser.add_argument(
'--sync-bn',
type=bool,
default=False,
help='sync-bn in deeplabv3+',
)
parser.add_argument(
'--freeze-bn',
type=bool,
default=False,
help='freeze batch normalization of deeplabv3+',
)
parser.add_argument('--test-prediction-save-path', type=str,
default='./results/baseline/',
help='Path root for test image and mask')
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
model_file = args.model_file
# 1. dataset
composed_transforms_test = transforms.Compose([
tr.Scale(args.resize),
tr.Normalize_tf(),
tr.ToTensor()
])
db_test = DL.FundusSegmentation(base_dir=args.data_dir, dataset=args.dataset, split='test',
transform=composed_transforms_test)
test_loader = DataLoader(db_test, batch_size=1, shuffle=False, num_workers=4, pin_memory=True)
# 2. model
model = DeepLab(num_classes=2, backbone='mobilenet', output_stride=args.out_stride,
sync_bn=args.sync_bn, freeze_bn=args.freeze_bn).cuda()
if torch.cuda.is_available():
model = model.cuda()
print('==> Loading %s model file: %s' %
(model.__class__.__name__, model_file))
checkpoint = torch.load(model_file)
# try:
# model.load_state_dict(checkpoint)
# pretrained_dict = checkpoint['model_state_dict']
# model_dict = model.state_dict()
# # 1. filter out unnecessary keys
# pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
# # 2. overwrite entries in the existing state dict
# model_dict.update(pretrained_dict)
# # 3. load the new state dict
# model.load_state_dict(model_dict)
# except Exception:
try:
model.load_state_dict(checkpoint['model_state_dict'])
except:
raise FileNotFoundError('No checkpoint file exist...')
model.eval()
print('==> Evaluating with %s' % args.dataset)
test_cup_dice = 0.0
test_disc_dice = 0.0
timestamp_start = \
datetime.now(pytz.timezone('Asia/Hong_Kong'))
with torch.no_grad():
for batch_idx, (sample) in tqdm.tqdm(enumerate(test_loader),
total=len(test_loader),
ncols=80, leave=False):
data = sample['image']
target = sample['map']
img_name = sample['img_name']
if torch.cuda.is_available():
data, target = data.cuda(), target.cuda()
# data, target = Variable(data), Variable(target)
prediction, boundary = model(data)
prediction = torch.nn.functional.interpolate(prediction, size=(target.size()[2], target.size()[3]),
mode="bilinear")
# boundary = torch.nn.functional.interpolate(boundary, size=(target.size()[2], target.size()[3]),
# mode="bilinear")
data = torch.nn.functional.interpolate(data, size=(target.size()[2], target.size()[3]), mode="bilinear")
cup_dice, disc_dice = dice_coeff_2label(prediction, target)
test_cup_dice += cup_dice
test_disc_dice += disc_dice
# boundary = torch.sigmoid(boundary)
# # drawing figures
# draw_ent(prediction.data.cpu()[0].numpy(), os.path.join(args.save_root_ent, args.dataset), img_name[0])
# draw_mask(prediction.data.cpu()[0].numpy(), os.path.join(args.save_root_mask, args.dataset), img_name[0])
# draw_boundary(boundary.data.cpu()[0].numpy(), os.path.join(args.save_root_mask, args.dataset), img_name[0])
prediction, ROI_mask = postprocessing(torch.sigmoid(prediction).data.cpu()[0], dataset=args.dataset)
imgs = data.data.cpu()
target_numpy = target.cpu().numpy()
for img, lt, lp in zip(imgs, target_numpy, [prediction]):
img, lt = untransform(img, lt)
save_per_img(img.numpy().transpose(1, 2, 0), os.path.join(args.test_prediction_save_path, args.dataset),
img_name[0], lp, lt, ROI_mask)
test_cup_dice /= len(test_loader)
test_disc_dice /= len(test_loader)
print("test_cup_dice = ", test_cup_dice)
print("test_disc_dice = ", test_disc_dice)
# submit script
_, _, mae_cdr = evaluate_segmentation_results(osp.join(args.test_prediction_save_path, args.dataset, 'pred_mask'),
args.mask_dir, output_path="./", export_table=True)
with open(osp.join(args.test_prediction_save_path, 'test_log.csv'), 'a') as f:
elapsed_time = (
datetime.now(pytz.timezone('Asia/Hong_Kong')) -
timestamp_start).total_seconds()
log = [[args.model_file] + ['cup dice: '] + \
[test_cup_dice] + ['disc dice: '] + \
[test_disc_dice] + ['cdr: '] + \
[mae_cdr] + [elapsed_time]]
log = map(str, log)
f.write(','.join(log) + '\n')
def main():
# Add default values to all parameters
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument('-g', '--gpu', type=int, default=0, help='gpu id')
parser.add_argument('--resume', default=None, help='checkpoint path')
parser.add_argument(
'--coefficient', type=float, default=0.01, help='balance coefficient'
)
parser.add_argument(
'--boundary-exist', type=bool, default=True, help='whether or not using boundary branch'
)
parser.add_argument(
'--dataset', type=str, default='refuge', help='folder id contain images ROIs to train or validation'
)
parser.add_argument(
'--batch-size', type=int, default=12, help='batch size for training the model'
)
# parser.add_argument(
# '--group-num', type=int, default=1, help='group number for group normalization'
# )
parser.add_argument(
'--max-epoch', type=int, default=300, help='max epoch'
)
parser.add_argument(
'--stop-epoch', type=int, default=300, help='stop epoch'
)
parser.add_argument(
'--warmup-epoch', type=int, default=-1, help='warmup epoch begin train GAN'
)
parser.add_argument(
'--interval-validate', type=int, default=1, help='interval epoch number to valide the model'
)
parser.add_argument(
'--lr-gen', type=float, default=1e-3, help='learning rate',
)
parser.add_argument(
'--lr-dis', type=float, default=2.5e-5, help='learning rate',
)
parser.add_argument(
'--lr-decrease-rate', type=float, default=0.2, help='ratio multiplied to initial lr',
)
parser.add_argument(
'--weight-decay', type=float, default=0.0005, help='weight decay',
)
parser.add_argument(
'--momentum', type=float, default=0.9, help='momentum',
)
parser.add_argument(
'--data-dir',
default='./fundus/',
help='data root path'
)
parser.add_argument(
'--out-stride',
type=int,
default=16,
help='out-stride of deeplabv3+',
)
parser.add_argument(
'--sync-bn',
type=bool,
default=False,
help='sync-bn in deeplabv3+',
)
parser.add_argument(
'--freeze-bn',
type=bool,
default=False,
help='freeze batch normalization of deeplabv3+',
)
args = parser.parse_args()
args.model = 'MobileNetV2'
now = datetime.now()
args.out = osp.join(here, 'logs', args.dataset, now.strftime('%Y%m%d_%H%M%S.%f'))
os.makedirs(args.out)
# save training hyperparameters or/and settings
with open(osp.join(args.out, 'config.yaml'), 'w') as f:
yaml.safe_dump(args.__dict__, f, default_flow_style=False)
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
cuda = torch.cuda.is_available()
torch.manual_seed(2020)
if cuda:
torch.cuda.manual_seed(2020)
import random
import numpy as np
random.seed(2020)
np.random.seed(2020)
# 1. loading data
composed_transforms_train = transforms.Compose([
tr.RandomScaleCrop(512),
tr.RandomRotate(),
tr.RandomFlip(),
tr.elastic_transform(),
tr.add_salt_pepper_noise(),
tr.adjust_light(),
tr.eraser(),
tr.Normalize_tf(),
tr.ToTensor()
])
composed_transforms_val = transforms.Compose([
tr.RandomCrop(512),
tr.Normalize_tf(),
tr.ToTensor()
])
data_train = DL.FundusSegmentation(base_dir=args.data_dir, dataset=args.dataset, split='train',
transform=composed_transforms_train)
dataloader_train = DataLoader(data_train, batch_size=args.batch_size, shuffle=True, num_workers=4,
pin_memory=True)
data_val = DL.FundusSegmentation(base_dir=args.data_dir, dataset=args.dataset, split='testval',
transform=composed_transforms_val)
dataloader_val = DataLoader(data_val, batch_size=args.batch_size, shuffle=False, num_workers=4, pin_memory=True)
# domain_val = DL.FundusSegmentation(base_dir=args.data_dir, dataset=args.datasetT, split='train',
# transform=composed_transforms_ts)
# domain_loader_val = DataLoader(domain_val, batch_size=args.batch_size, shuffle=False, num_workers=2,
# pin_memory=True)
# 2. model
model_gen = DeepLab(num_classes=2, backbone='mobilenet', output_stride=args.out_stride,
sync_bn=args.sync_bn, freeze_bn=args.freeze_bn).cuda()
model_bd = BoundaryDiscriminator().cuda()
model_mask = MaskDiscriminator().cuda()
start_epoch = 0
start_iteration = 0
# 3. optimizer
optim_gen = torch.optim.Adam(
model_gen.parameters(),
lr=args.lr_gen,
betas=(0.9, 0.99)
)
optim_bd = torch.optim.SGD(
model_bd.parameters(),
lr=args.lr_dis,
momentum=args.momentum,
weight_decay=args.weight_decay
)
optim_mask = torch.optim.SGD(
model_mask.parameters(),
lr=args.lr_dis,
momentum=args.momentum,
weight_decay=args.weight_decay
)
# breakpoint recovery
if args.resume:
checkpoint = torch.load(args.resume)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model_gen.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model_gen.load_state_dict(model_dict)
pretrained_dict = checkpoint['model_bd_state_dict']
model_dict = model_bd.state_dict()
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
model_dict.update(pretrained_dict)
model_bd.load_state_dict(model_dict)
pretrained_dict = checkpoint['model_mask_state_dict']
model_dict = model_mask.state_dict()
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
model_dict.update(pretrained_dict)
model_mask.load_state_dict(model_dict)
start_epoch = checkpoint['epoch'] + 1
start_iteration = checkpoint['iteration'] + 1
optim_gen.load_state_dict(checkpoint['optim_state_dict'])
optim_bd.load_state_dict(checkpoint['optim_bd_state_dict'])
optim_mask.load_state_dict(checkpoint['optim_mask_state_dict'])
trainer = Trainer.Trainer(
cuda=cuda,
model_gen=model_gen,
model_bd=model_bd,
model_mask=model_mask,
optimizer_gen=optim_gen,
optim_bd=optim_bd,
optim_mask=optim_mask,
lr_gen=args.lr_gen,
lr_dis=args.lr_dis,
lr_decrease_rate=args.lr_decrease_rate,
train_loader=dataloader_train,
validation_loader=dataloader_val,
out=args.out,
max_epoch=args.max_epoch,
stop_epoch=args.stop_epoch,
interval_validate=args.interval_validate,
batch_size=args.batch_size,
warmup_epoch=args.warmup_epoch,
coefficient=args.coefficient,
boundary_exist=args.boundary_exist
)
trainer.epoch = start_epoch
trainer.iteration = start_iteration
trainer.train()
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter, )
parser.add_argument('-g', '--gpu', type=int, default=0, help='gpu id')
parser.add_argument('--resume', default=None, help='checkpoint path')
# configurations (same configuration as original work)
# https://github.com/shelhamer/fcn.berkeleyvision.org
parser.add_argument('--datasetS',
type=str,
default='refuge',
help='test folder id contain images ROIs to test')
parser.add_argument('--datasetT',
type=str,
default='Drishti-GS',
help='refuge / Drishti-GS/ RIM-ONE_r3')
parser.add_argument('--batch-size',
type=int,
default=8,
help='batch size for training the model')
parser.add_argument('--group-num',
type=int,
default=1,
help='group number for group normalization')
parser.add_argument('--max-epoch', type=int, default=200, help='max epoch')
parser.add_argument('--stop-epoch',
type=int,
default=200,
help='stop epoch')
parser.add_argument('--warmup-epoch',
type=int,
default=-1,
help='warmup epoch begin train GAN')
parser.add_argument('--interval-validate',
type=int,
default=10,
help='interval epoch number to valide the model')
parser.add_argument(
'--lr-gen',
type=float,
default=1e-3,
help='learning rate',
)
parser.add_argument(
'--lr-dis',
type=float,
default=2.5e-5,
help='learning rate',
)
parser.add_argument(
'--lr-decrease-rate',
type=float,
default=0.1,
help='ratio multiplied to initial lr',
)
parser.add_argument(
'--weight-decay',
type=float,
default=0.0005,
help='weight decay',
)
parser.add_argument(
'--momentum',
type=float,
default=0.99,
help='momentum',
)
parser.add_argument('--data-dir',
default='/home/sjwang/ssd1T/fundus/domain_adaptation/',
help='data root path')
parser.add_argument(
'--pretrained-model',
default='../../../models/pytorch/fcn16s_from_caffe.pth',
help='pretrained model of FCN16s',
)
parser.add_argument(
'--out-stride',
type=int,
default=16,
help='out-stride of deeplabv3+',
)
parser.add_argument(
'--sync-bn',
type=bool,
default=True,
help='sync-bn in deeplabv3+',
)
parser.add_argument(
'--freeze-bn',
type=bool,
default=False,
help='freeze batch normalization of deeplabv3+',
)
args = parser.parse_args()
args.model = 'FCN8s'
now = datetime.now()
args.out = osp.join(here, 'logs', args.datasetT,
now.strftime('%Y%m%d_%H%M%S.%f'))
os.makedirs(args.out)
with open(osp.join(args.out, 'config.yaml'), 'w') as f:
yaml.safe_dump(args.__dict__, f, default_flow_style=False)
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
cuda = torch.cuda.is_available()
torch.manual_seed(1337)
if cuda:
torch.cuda.manual_seed(1337)
# 1. dataset
composed_transforms_tr = transforms.Compose([
tr.RandomScaleCrop(512),
tr.RandomRotate(),
tr.RandomFlip(),
tr.elastic_transform(),
tr.add_salt_pepper_noise(),
tr.adjust_light(),
tr.eraser(),
tr.Normalize_tf(),
tr.ToTensor()
])
composed_transforms_ts = transforms.Compose(
[tr.RandomCrop(512),
tr.Normalize_tf(),
tr.ToTensor()])
domain = DL.FundusSegmentation(base_dir=args.data_dir,
dataset=args.datasetS,
split='train',
transform=composed_transforms_tr)
domain_loaderS = DataLoader(domain,
batch_size=args.batch_size,
shuffle=True,
num_workers=2,
pin_memory=True)
domain_T = DL.FundusSegmentation(base_dir=args.data_dir,
dataset=args.datasetT,
split='train',
transform=composed_transforms_tr)
domain_loaderT = DataLoader(domain_T,
batch_size=args.batch_size,
shuffle=False,
num_workers=2,
pin_memory=True)
domain_val = DL.FundusSegmentation(base_dir=args.data_dir,
dataset=args.datasetT,
split='train',
transform=composed_transforms_ts)
domain_loader_val = DataLoader(domain_val,
batch_size=args.batch_size,
shuffle=False,
num_workers=2,
pin_memory=True)
# 2. model
model_gen = DeepLab(num_classes=2,
backbone='mobilenet',
output_stride=args.out_stride,
sync_bn=args.sync_bn,
freeze_bn=args.freeze_bn).cuda()
model_dis = BoundaryDiscriminator().cuda()
model_dis2 = UncertaintyDiscriminator().cuda()
start_epoch = 0
start_iteration = 0
# 3. optimizer
optim_gen = torch.optim.Adam(model_gen.parameters(),
lr=args.lr_gen,
betas=(0.9, 0.99))
optim_dis = torch.optim.SGD(model_dis.parameters(),
lr=args.lr_dis,
momentum=args.momentum,
weight_decay=args.weight_decay)
optim_dis2 = torch.optim.SGD(model_dis2.parameters(),
lr=args.lr_dis,
momentum=args.momentum,
weight_decay=args.weight_decay)
if args.resume:
checkpoint = torch.load(args.resume)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model_gen.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {
k: v
for k, v in pretrained_dict.items() if k in model_dict
}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model_gen.load_state_dict(model_dict)
pretrained_dict = checkpoint['model_dis_state_dict']
model_dict = model_dis.state_dict()
pretrained_dict = {
k: v
for k, v in pretrained_dict.items() if k in model_dict
}
model_dict.update(pretrained_dict)
model_dis.load_state_dict(model_dict)
pretrained_dict = checkpoint['model_dis2_state_dict']
model_dict = model_dis2.state_dict()
pretrained_dict = {
k: v
for k, v in pretrained_dict.items() if k in model_dict
}
model_dict.update(pretrained_dict)
model_dis2.load_state_dict(model_dict)
start_epoch = checkpoint['epoch'] + 1
start_iteration = checkpoint['iteration'] + 1
optim_gen.load_state_dict(checkpoint['optim_state_dict'])
optim_dis.load_state_dict(checkpoint['optim_dis_state_dict'])
optim_dis2.load_state_dict(checkpoint['optim_dis2_state_dict'])
optim_adv.load_state_dict(checkpoint['optim_adv_state_dict'])
trainer = Trainer.Trainer(
cuda=cuda,
model_gen=model_gen,
model_dis=model_dis,
model_uncertainty_dis=model_dis2,
optimizer_gen=optim_gen,
optimizer_dis=optim_dis,
optimizer_uncertainty_dis=optim_dis2,
lr_gen=args.lr_gen,
lr_dis=args.lr_dis,
lr_decrease_rate=args.lr_decrease_rate,
val_loader=domain_loader_val,
domain_loaderS=domain_loaderS,
domain_loaderT=domain_loaderT,
out=args.out,
max_epoch=args.max_epoch,
stop_epoch=args.stop_epoch,
interval_validate=args.interval_validate,
batch_size=args.batch_size,
warmup_epoch=args.warmup_epoch,
)
trainer.epoch = start_epoch
trainer.iteration = start_iteration
trainer.train()
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter, )
parser.add_argument('-g', '--gpu', type=int, default=0, help='gpu id')
parser.add_argument('--resume', default=None, help='checkpoint path')
parser.add_argument(
'--datasetTrain',
nargs='+',
type=int,
default=1,
help='train folder id contain images ROIs to train range from [1,2,3,4]'
)
parser.add_argument(
'--datasetTest',
nargs='+',
type=int,
default=1,
help='test folder id contain images ROIs to test one of [1,2,3,4]')
parser.add_argument('--batch-size',
type=int,
default=8,
help='batch size for training the model')
parser.add_argument('--group-num',
type=int,
default=1,
help='group number for group normalization')
parser.add_argument('--max-epoch', type=int, default=120, help='max epoch')
parser.add_argument('--stop-epoch',
type=int,
default=80,
help='stop epoch')
parser.add_argument('--interval-validate',
type=int,
default=10,
help='interval epoch number to valide the model')
parser.add_argument(
'--lr',
type=float,
default=1e-3,
help='learning rate',
)
parser.add_argument('--lr-decrease-rate',
type=float,
default=0.2,
help='ratio multiplied to initial lr')
parser.add_argument(
'--lam',
type=float,
default=0.9,
help='momentum of memory update',
)
parser.add_argument('--data-dir',
default='../../../../Dataset/Fundus/',
help='data root path')
parser.add_argument(
'--pretrained-model',
default='../../../models/pytorch/fcn16s_from_caffe.pth',
help='pretrained model of FCN16s',
)
parser.add_argument(
'--out-stride',
type=int,
default=16,
help='out-stride of deeplabv3+',
)
args = parser.parse_args()
now = datetime.now()
args.out = osp.join(local_path, 'logs', 'test' + str(args.datasetTest[0]),
'lam' + str(args.lam),
now.strftime('%Y%m%d_%H%M%S.%f'))
os.makedirs(args.out)
with open(osp.join(args.out, 'config.yaml'), 'w') as f:
yaml.safe_dump(args.__dict__, f, default_flow_style=False)
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
cuda = torch.cuda.is_available()
torch.cuda.manual_seed(1337)
# 1. dataset
composed_transforms_tr = transforms.Compose([
tr.RandomScaleCrop(256),
# tr.RandomCrop(512),
# tr.RandomRotate(),
# tr.RandomFlip(),
# tr.elastic_transform(),
# tr.add_salt_pepper_noise(),
# tr.adjust_light(),
# tr.eraser(),
tr.Normalize_tf(),
tr.ToTensor()
])
composed_transforms_ts = transforms.Compose(
[tr.RandomCrop(256),
tr.Normalize_tf(),
tr.ToTensor()])
domain = DL.FundusSegmentation(base_dir=args.data_dir,
phase='train',
splitid=args.datasetTrain,
transform=composed_transforms_tr)
train_loader = DataLoader(domain,
batch_size=args.batch_size,
shuffle=True,
num_workers=2,
pin_memory=True)
domain_val = DL.FundusSegmentation(base_dir=args.data_dir,
phase='test',
splitid=args.datasetTest,
transform=composed_transforms_ts)
val_loader = DataLoader(domain_val,
batch_size=args.batch_size,
shuffle=False,
num_workers=2,
pin_memory=True)
# 2. model
model = DeepLab(num_classes=2,
num_domain=3,
backbone='mobilenet',
output_stride=args.out_stride,
lam=args.lam).cuda()
print('parameter numer:', sum([p.numel() for p in model.parameters()]))
# load weights
if args.resume:
checkpoint = torch.load(args.resume)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {
k: v
for k, v in pretrained_dict.items() if k in model_dict
}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model.load_state_dict(model_dict)
print('Before ', model.centroids.data)
model.centroids.data = centroids_init(model, args.data_dir,
args.datasetTrain,
composed_transforms_ts)
print('Before ', model.centroids.data)
# model.freeze_para()
start_epoch = 0
start_iteration = 0
# 3. optimizer
optim = torch.optim.Adam(model.parameters(), lr=args.lr, betas=(0.9, 0.99))
trainer = Trainer.Trainer(
cuda=cuda,
model=model,
lr=args.lr,
lr_decrease_rate=args.lr_decrease_rate,
train_loader=train_loader,
val_loader=val_loader,
optim=optim,
out=args.out,
max_epoch=args.max_epoch,
stop_epoch=args.stop_epoch,
interval_validate=args.interval_validate,
batch_size=args.batch_size,
)
trainer.epoch = start_epoch
trainer.iteration = start_iteration
trainer.train()
