def validate(val_loader, model, criterion):
# list to store the losses and accuracies: [loss, pixel_acc, iou ]
results = utils.AverageMeter(3)
# switch to evaluate mode
model.eval()
for i, sample in enumerate(val_loader):
input, weight_map, target = sample
weight_map = weight_map.float().div(20)
if weight_map.dim() == 4:
weight_map = weight_map.squeeze(1)
weight_map_var = weight_map.cuda()
# for b in range(input.size(0)):
# utils.show_figures((input[b, 0, :, :].numpy(), target[b,0,:,:].numpy(), weight_map[b, :, :]))
if torch.max(target) == 255:
target = target / 255
if target.dim() == 4:
target = target.squeeze(1)
target_var = target.cuda()
size = opt.train['input_size']
overlap = opt.train['val_overlap']
output = utils.split_forward(model, input, size, overlap, opt.model['out_c'])
log_prob_maps = F.log_softmax(output, dim=1)
loss_map = criterion(log_prob_maps, target_var)
loss_map *= weight_map_var
loss_CE = loss_map.mean()
if opt.train['alpha'] != 0:
prob_maps = F.softmax(output, dim=1)
target_labeled = torch.zeros(target.size()).long()
for k in range(target.size(0)):
target_labeled[k] = torch.from_numpy(measure.label(target[k].numpy() == 1))
# utils.show_figures((target[k].numpy(), target[k].numpy()==1, target_labeled[k].numpy()))
loss_var = criterion_var(prob_maps, target_labeled.cuda())
loss = loss_CE + opt.train['alpha'] * loss_var
else:
loss = loss_CE
# measure accuracy and record loss
pred = np.argmax(log_prob_maps.data.cpu().numpy(), axis=1)
metrics = utils.accuracy_pixel_level(pred, target.numpy())
pixel_accu = metrics[0]
iou = metrics[1]
results.update([loss.item(), pixel_accu, iou])
del output, target_var, log_prob_maps, loss
logger.info('\t=> Val Avg: Loss {r[0]:.4f}\tPixel_Acc {r[1]:.4f}'
'\tIoU {r[2]:.4f}'.format(r=results.avg))
return results.avg
def get_probmaps(input, model, opt):
size = opt.test['patch_size']
overlap = opt.test['overlap']
output = utils.split_forward(model, input, size, overlap, with_uncertainty=False)
output = output.squeeze(0)
prob_maps = F.softmax(output, dim=0).cpu().numpy()
return prob_maps
def get_probmaps(input, model, opt):
size = opt.test['patch_size']
overlap = opt.test['overlap']
if size == 0:
with torch.no_grad():
output = model(input.cuda())
else:
output = utils.split_forward(model, input, size, overlap)
output = output.squeeze(0)
prob_maps = F.softmax(output, dim=0).cpu().numpy()
return prob_maps
def get_probmaps(input, model, opt):
size = opt.test['patch_size']
overlap = opt.test['overlap']
if size == 0:
with torch.no_grad():
output = model(input.cuda())
else:
output = utils.split_forward(model, input, size, overlap,
opt.model['out_c'])
output = torch.sigmoid(output[0, 0, :, :]).cpu().numpy()
return output
def get_probmaps(input, model, opt):
size = opt.test['patch_size']
overlap = opt.test['overlap']
if size == 0:
with torch.no_grad():
output = model(input.cuda())
else:
output = utils.split_forward(model, input, size, overlap)
output = output.squeeze(0)
prob_maps = torch.sigmoid(output[0, :, :])
return prob_maps
def get_probmaps(input, model, opt):
size = opt.test['patch_size']
overlap = opt.test['overlap']
output, log_var = utils.split_forward(model,
input,
size,
overlap,
with_uncertainty=True)
output = output.squeeze(0)
log_var = log_var.squeeze(0)
return output.cpu().numpy(), log_var.cpu().numpy()
def validate(val_loader, model, criterion):
# list to store the losses and accuracies: [loss, pixel_acc, iou ]
results = utils.AverageMeter(5)
# switch to evaluate mode
model.eval()
for i, sample in enumerate(val_loader):
if params.train['weight_map']:
input, weight_map, target = sample
weight_map = weight_map.float().div(20)
if weight_map.dim() == 4:
weight_map = weight_map.squeeze(1)
weight_map_var = weight_map.cuda()
else:
input, target = sample
# no classification
if params.model['out_c'] == 3:
target[target == 2] = 1
target[target == 3] = 1
target[target == 4] = 2
# no edge or classification
if params.model['out_c'] == 2:
target[target > 0] = 1
if target.dim() == 4:
target = target.squeeze(1)
target_var = target.cuda()
size = params.train['input_size']
overlap = params.train['val_overlap']
output = utils.split_forward(model, input, size, overlap,
params.model['out_c'])
log_prob_maps = F.log_softmax(output, dim=1)
if params.train['weight_map']:
loss_map = criterion(log_prob_maps, target_var)
loss_map *= weight_map_var
loss_CE = loss_map.sum() / (loss_map.size(0) * loss_map.size(1) *
loss_map.size(2))
else:
loss_CE = criterion(log_prob_maps, target_var)
loss = loss_CE
if params.train['beta'] != 0:
prob_maps = F.softmax(output, dim=1)
pred_map = prob_maps[:, 4:5, :, :].repeat(1, 3, 1, 1).float()
target_map = (target_var == 4).unsqueeze(1).repeat(1, 3, 1,
1).float()
pred_feat = vgg_model(pred_map)
target_feat = vgg_model(target_map)
loss_perceptual = criterion_perceptual(pred_feat, target_feat)
loss = loss_CE + params.train['beta'] * loss_perceptual
# measure accuracy and record loss
pred = np.argmax(log_prob_maps.data.cpu().numpy(), axis=1)
iou = utils.accuracy(pred,
target.numpy(),
num_class=params.model['out_c'] - 1)
if params.model['out_c'] == 5:
iou_nuclei = utils.accuracy(np.uint8((pred > 0) * (pred < 4)),
np.uint8((target.numpy() > 0) *
(target.numpy() < 4)),
num_class=2)
else:
iou_nuclei = utils.accuracy(np.uint8((pred == 1)),
np.uint8((target.numpy() == 1)),
num_class=2)
if params.train['beta'] != 0:
result = [
loss.item(),
loss_CE.item(),
loss_perceptual.item(), iou_nuclei, iou
]
else:
result = [loss.item(), loss_CE.item(), 0, iou_nuclei, iou]
results.update(result, input.size(0))
del output, target_var, log_prob_maps, loss
logger.info('\t=> Val Avg: Loss {r[0]:.4f}'
'\tLoss_CE {r[1]:.4f}'
'\tLoss_Per {r[2]:.4f}'
'\tIoU-nuclei {r[3]:.4f}'
'\tIoU {r[4]:.4f}'.format(r=results.avg))
return results.avg
