def show_features(load, encoder=0, xslice=20):
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
model = init_forknet(load, device)
activation = {}
def get_activation(name):
def hook(model, input, output):
activation[name] = output.detach()
return hook
# encode[0] is the convolution module of the encoder
model.encoders[encoder].encode[0].register_forward_hook(
get_activation('enc1'))
dataset = MICCAI18(base_dir="./data/miccai18/training",
case_list=['4'],
slice_axis=2)
loader = torch.utils.data.DataLoader(dataset,
num_workers=2,
batch_size=48,
shuffle=True)
batch_dict = iter(loader).next()
for tensor in batch_dict:
batch_dict[tensor] = batch_dict[tensor].to(device)
data = batch_dict['t1w'][xslice]
data.unsqueeze_(0)
output = model(data)
act = activation['enc1'].squeeze()
num_plots = 2
fig, axarr = plt.subplots(ncols=num_plots)
for idx in range(num_plots):
axarr[idx].imshow(act[idx].detach().cpu())
plt.show()
def train(epoch):
model.train()
train_loss, train_prior_loss, train_likelihood = 0, 0, 0
# for batch_idx, (data, _) in enumerate(train_loader):
for batch_idx, data in enumerate(train_loader):
data.transpose_(0, 1)
data.unsqueeze_(2)
data = Variable(data[0])
if args.cuda:
data = data.cuda()
optimizer.zero_grad()
recon_batch, mu, logvar = model(data)
loss, prior, likelihood = loss_function(recon_batch, data, mu, logvar)
loss.backward()
train_loss += loss.data[0]
train_prior_loss += prior.data[0]
train_likelihood += likelihood.data[0]
optimizer.step()
if batch_idx % args.log_interval == 0:
print('Train Epoch: {} [{}/{} ({:.0f}%)]\tLoss: {:.6f}'.format(
epoch, batch_idx * len(data), len(train_loader.dataset),
100. * batch_idx / len(train_loader),
loss.data[0]))
train_loss /= (len(train_loader.dataset) / args.batch_size)
train_prior_loss /= (len(train_loader.dataset) / args.batch_size)
train_likelihood /= (len(train_loader.dataset) / args.batch_size)
print('====> Epoch: {} Average loss: {:.4f}'.format(
epoch, train_loss))
return train_loss, train_prior_loss, train_likelihood
def train(epoch):
model.train()
total_loss = 0.0
global optimizer
global prev_loss
for batch_idx, (data, target) in enumerate(train_loader):
if args.cuda:
data, target = data.cuda(), target.cuda()
data = data.unsqueeze_(1)
data, target = Variable(data), Variable(target)
optimizer.zero_grad()
output = model(data)
loss = F.nll_loss(output, target)
total_loss += loss.item() # loss.data[0]
loss.backward()
optimizer.step()
if batch_idx % args.log_interval == 0:
print('Train Epoch: {} [{}/{} ({:.0f}%)]\tLoss: {:.6f}'.format(
epoch, batch_idx * len(data), len(train_loader.dataset),
100. * batch_idx / len(train_loader),
loss.item())) # loss.data[0]))
print("Total loss = %.6f" % (total_loss / len(train_loader.dataset)))
dev_loss = 0.
model.eval()
f = open('dev-eer', 'w')
for data, devtarget in devdata_loader:
data = data.unsqueeze_(1)
data, target = Variable(data), Variable(devtarget)
if args.cuda:
data, target = data.cuda(), target.cuda()
output = model(data)
if args.cuda:
op = output.cpu()
tgt = target.cpu()
else:
op = output
tgt = target
output_arr = op.data.numpy().reshape((-1, 2))
tgt = tgt.data.numpy()
for i in range(tgt.shape[0]):
itgt = int(tgt[i])
scr = -output_arr[i, 0] + output_arr[i, 1]
if itgt == 0:
f.write('%f %s\n' % (scr, 'nontarget'))
else:
f.write('%f %s\n' % (scr, 'target'))
dev_loss += F.nll_loss(output, target,
size_average=False).item() # sum up batch loss
f.close()
dev_loss /= len(devdata_loader.dataset)
print("Dev loss is %.6f" % dev_loss)
def test():
model.eval()
test_loss = 0
correct = 0
f = open('eer-file', 'w')
for data, target in test_loader:
if args.cuda:
data, target = data.cuda(), target.cuda()
data = data.unsqueeze_(1)
data, target = Variable(data, volatile=True), Variable(target)
output = model(data)
output_arr = output.data.numpy().reshape((-1, 2))
tgt = target.data.numpy()
for i in range(tgt.shape[0]):
itgt = int(tgt[i])
scr = -output_arr[i, 0] + output_arr[i, 1]
if itgt == 0:
f.write('%f %s\n' % (scr, 'nontarget'))
else:
f.write('%f %s\n' % (scr, 'target'))
test_loss += F.nll_loss(output, target,
size_average=False).item() # sum up batch loss
pred = output.data.max(
1, keepdim=True)[1] # get the index of the max log-probability
correct += pred.eq(target.data.view_as(pred)).cpu().sum()
f.close()
test_loss /= len(test_loader.dataset)
print(
'\nTest set: Average loss: {:.4f}, Accuracy: {}/{} ({:.0f}%)\n'.format(
test_loss, correct, len(test_loader.dataset),
100. * correct / len(test_loader.dataset)))
def train(epochs, train_loader, dev_loader, lr, seed, log_interval,
output_dir):
"""Train the model. Store snapshot models in the output_dir alongside
evaluations on the dev set after each epoch
"""
model = Net()
optimizer = optim.Adam(model.parameters(), lr=lr)
measure_size(model)
use_cuda = torch.cuda.is_available()
device = torch.device("cuda:0" if use_cuda else "cpu")
print("Using device: ", device)
if use_cuda:
torch.cuda.manual_seed(seed)
else:
torch.manual_seed(seed)
#torch.backends.cudnn.benchmark = False
#torch.backends.cudnn.deterministic = True
model.to(device)
for epoch in range(1, epochs):
model.train()
total_loss = 0.0
for batch_idx, (data, target) in enumerate(train_loader):
if use_cuda:
data, target = data.to(device), target.to(device)
data = data.unsqueeze_(1)
optimizer.zero_grad()
output = model(data)
loss = F.nll_loss(output, target)
total_loss += loss.item()
loss.backward()
optimizer.step()
if batch_idx % log_interval == 0:
print('Train Epoch: {} [{}/{} ({:.0f}%)]\tLoss: {:.6f}'.format(
epoch, batch_idx * len(data), len(train_loader.dataset),
100. * batch_idx / len(train_loader), loss.item()))
print("Total loss = %.6f" % (total_loss / len(train_loader.dataset)))
test(model, dev_loader,
os.path.join(output_dir, 'dev-eer-' + str(epoch)))
torch.save(model, os.path.join(output_dir,
'iter' + str(epoch) + '.mdl'))
def test(model, test_loader, report_filename):
"""Test the model on a provided dataset
Save test output to a `report_filename`.
Print a summary of performance to stdout.
"""
model.eval()
test_loss = 0
correct = 0
scores = []
targets = []
use_cuda = torch.cuda.is_available()
device = torch.device("cuda:0" if use_cuda else "cpu")
with open(report_filename, 'w') as f:
for data, target in test_loader:
if use_cuda:
data, target = data.to(device), target.to(device)
data = data.unsqueeze_(1)
output = model(data)
if use_cuda:
op = output.cpu()
tgt = target.cpu()
else:
op = output
tgt = target
output_arr = op.data.numpy().reshape((-1, 2))
tgt = tgt.data.numpy()
for i in range(tgt.shape[0]):
itgt = int(tgt[i])
scr = -output_arr[i, 0] + output_arr[i, 1]
t = "nontarget" if itgt == 0 else "target"
f.write('%f %s\n' % (scr, t))
scores.append(scr)
targets.append(t)
test_loss += F.nll_loss(
output, target, reduction='sum').item() # sum up batch loss
pred = output.data.max(
1, keepdim=True)[1] # get the index of the max log-probability
correct += pred.eq(target.data.view_as(pred)).cpu().sum()
test_eer = eer(targets, scores)
test_loss /= len(test_loader.dataset)
print(
'\nTest set: Average loss: {:.4f}, Accuracy: {}/{} ({:.0f}%), EER: {}%\n'
.format(test_loss, correct, len(test_loader.dataset),
100. * correct / len(test_loader.dataset), test_eer * 100))
def test(epoch):
model.eval()
test_loss, test_prior_loss, test_likelihood = 0, 0, 0
# for data, _ in test_loader:
for data in test_loader:
data.transpose_(0, 1)
data.unsqueeze_(2)
if args.cuda:
data = data.cuda()
data = Variable(data[0], volatile=True)
recon_batch, mu, logvar = model(data)
loss, prior, likelihood = loss_function(recon_batch, data, mu, logvar)
test_loss += loss.data[0]
test_prior_loss += prior.data[0]
test_likelihood += likelihood.data[0]
test_loss /= (len(test_loader.dataset) / args.batch_size)
test_prior_loss /= (len(test_loader.dataset) / args.batch_size)
test_likelihood /= (len(test_loader.dataset) / args.batch_size)
print('====> Test set loss: {:.4f}'.format(test_loss))
return test_loss, test_prior_loss, test_likelihood
def train(model, trainData, testData, optimizer, criterion):
trainLoss = 0
correct = 0
for idx, (data, target) in enumerate(trainData):
model.train()
data, target = data.cuda(), target.long().cuda()
optimizer.zero_grad()
output = model(data.unsqueeze_(1))
loss = criterion(output, target)
pred = output.argmax(dim=1, keepdim=True)
correct += pred.eq(target.view_as(pred)).sum().item()
trainLoss += loss.item()
loss.backward()
optimizer.step()
return trainLoss, 100. * (correct / len(trainData.dataset))
def predict(arc):
args = parser.parse_args()
args.arch = arc
f_out = open('submission/round2_%s_log_submission.csv' % (arc), 'w')
for i in range(len(task_list)):
task = task_list[i]
args.task = task
model, input_size = get_model(args)
input_size = 512
model = nn.DataParallel(model, device_ids=CUDDEVICE).cuda()
checkpoint_name = os.path.join('./round2_checkpoint',
arc + '_' + task + '_best.pkl')
checkpoint = torch.load(checkpoint_name)
# print(task + ' : ' + str(checkpoint['best_prec1']))
# continue
model.module.load_state_dict(checkpoint['state_dict'])
#model.cpu()
criterion = nn.CrossEntropyLoss().cuda()
#model = model.cuda()
model.eval()
# if arc == 'resnet50' or arc =='inceptionv4' or arc =='resnet152':
# # model._modules.module.module.fc = model._modules.module.module.last_linear
# model.module.module.fc = model.module.module.last_linear
# if arc == 'densenet169':
# model.classifier = model.last_linear
# if arc == 'xception':
# model.last_linear = model.fc
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
transform = transforms.Compose([
transforms.Resize((input_size, input_size)),
transforms.ToTensor(),
normalize,
])
# f_out = open('submission/%s_%s.csv' % (arc, task), 'w')
with open('data/week-rank/Tests/question.csv', 'r') as f_in:
lines = f_in.readlines()
tokens = [l.rstrip().split(',') for l in lines]
task_tokens = [t for t in tokens if t[1] == task]
n = len(task_tokens)
cnt = 0
for path, task, _ in task_tokens:
img_path = os.path.join('data/week-rank', path)
img = Image.open(img_path)
data = transform(img)
data = data.unsqueeze_(0)
data = data.cuda(async=True)
data = Variable(data, volatile=True)
output = model(data)
# softmax = torch.nn.Softmax(dim=-1)
softmax = torch.nn.LogSoftmax(dim=-1)
output = softmax(output)
output = output.view(-1)
output = output.cpu().data.numpy().tolist()
print(output, path)
pred_out = ';'.join(["%.8f" % (o) for o in output])
line_out = ','.join([path, task, pred_out])
f_out.write(line_out + '\n')
cnt += 1
progressbar(cnt, n)
f_out.close()
for epoch in range(1, args.epochs + 1):
train_loss, train_prior_loss, train_likelihood = train(epoch)
test_loss, test_prior_loss, test_likelihood = test(epoch)
log_values = (epoch, train_loss, train_prior_loss, train_prior_loss, train_likelihood, test_loss, test_prior_loss, test_likelihood)
format_string = ",".join(["{:.8e}"]*len(log_values))
logging.debug(format_string.format(*log_values))
z = Variable(torch.randn(args.batch_size, args.hidden_dim), volatile=True)
if args.cuda:
z = z.cuda()
# pdb.set_trace()
generations = model.decode(z)[0]
generations = generations.resize(generations.size(0), 28, 28)
for batch_idx, data in enumerate(train_loader):
data.transpose_(0, 1)
data.unsqueeze_(2)
data = Variable(data[0], volatile=True)
if args.cuda:
data = data.cuda()
recon_batch, mu, logvar = model(data)
recon_batch = recon_batch[0].data
recon_batch.resize_(recon_batch.size(0), 28, 28)
save_tensors_image("{}/recons{}.png".format(args.save, epoch),
[g.expand(3, 28, 28) for g in recon_batch])
break
save_tensors_image("{}/generations{}.png".format(args.save, epoch),
[g.expand(3, 28, 28) for g in generations])
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--workers', type=int, help='number of data loading workers', default=8)
parser.add_argument('--batchSize', type=int, default=64, help='input batch size')
parser.add_argument('--nz', type=int, default=8, help='size of the latent z vector')
parser.add_argument('--niter', type=int, default=25, help='number of epochs to train for')
parser.add_argument('--lr', type=float, default=0.00005, help='learning rate, default=0.0002')
parser.add_argument('--beta1', type=float, default=0.5, help='beta1 for adam. default=0.5')
parser.add_argument('--outf', default='./out/', help='folder to output images and model checkpoints')
parser.add_argument('--manualSeed', type=int, help='manual seed')
opt = parser.parse_args()
print(opt)
ngpu = 1
try:
os.makedirs(opt.outf)
except OSError:
pass
if opt.manualSeed is None:
opt.manualSeed = random.randint(1, 10000)
print("Random Seed: ", opt.manualSeed)
random.seed(opt.manualSeed)
torch.manual_seed(opt.manualSeed)
dataset = ds.MimicData()
assert dataset
dataloader = torch.utils.data.DataLoader(dataset, batch_size=opt.batchSize, shuffle=True, num_workers=int(opt.workers))
device = torch.device("cuda:0" if (torch.cuda.is_available() and ngpu > 0) else "cpu")
print(device)
nz = int(opt.nz)
ngf = 64
ndf = 64
nc = 1
# custom weights initialization called on netG and netD
# custom weights initialization called on netG and netD
def weights_init(m):
classname = m.__class__.__name__
if classname.find('Conv') != -1:
nn.init.normal_(m.weight.data, 0, 0.02)
elif classname.find('BatchNorm') != -1:
nn.init.normal_(m.weight.data, 1, 0.02)
nn.init.constant_(m.bias.data, 0)
class Generator(nn.Module):
def __init__(self):
super(Generator, self).__init__()
self.main = nn.Sequential(
nn.ConvTranspose2d(nz, ngf * 4, (1, 2), (1, 1), 0, bias=False),
nn.BatchNorm2d(ngf * 4),
nn.ReLU(True),
# state size. (ngf*8) x 4 x 4
nn.ConvTranspose2d(ngf * 4, ngf * 2, (1, 2), (1, 2), 0, bias=False),
nn.BatchNorm2d(ngf * 2),
nn.ReLU(True),
# state size. (ngf*4) x 8 x 8
nn.ConvTranspose2d(ngf * 2, ngf * 2, (1, 2), (1, 2), 0, bias=False),
nn.BatchNorm2d(ngf * 2),
nn.ReLU(True),
# state size. (ngf*2) x 16 x 16
nn.ConvTranspose2d(ngf * 2, ngf * 2, (1, 7), (1, 2), 0, bias=False),
nn.BatchNorm2d(ngf * 2),
nn.ReLU(True),
# state size. (ngf*2) x 16 x 16
nn.ConvTranspose2d(ngf * 2, ngf, (6, 1), (1, 1), 0, bias=False),
nn.BatchNorm2d(ngf),
nn.ReLU(True),
# state size. (ngf) x 32 x 32
nn.ConvTranspose2d(ngf, nc, (10, 1), (8, 1), 0, bias=False),
nn.Tanh()
# state size. (nc) x 64 x 64
)
def forward(self, input):
output = self.main(input)
return output
netG = Generator().to(device)
# Handle multi-gpu if desired
if (device.type == 'cuda') and (ngpu > 1):
netG = nn.DataParallel(netG, list(range(ngpu)))
netG.apply(weights_init)
class Discriminator(nn.Module):
def __init__(self):
super(Discriminator, self).__init__()
self.main = nn.Sequential(
# input is (nc) x 64 x 64
nn.Conv2d(nc, ndf, (10, 1), (8, 1), 0, bias=False),
nn.BatchNorm2d(ndf),
nn.LeakyReLU(0.2, inplace=True),
# state size. (ndf) x 32 x 32
nn.Conv2d(ndf, ndf * 2, (6, 1), (6, 1), 0, bias=False),
nn.BatchNorm2d(ndf * 2),
nn.LeakyReLU(0.2, inplace=True),
# state size. (ndf*2) x 16 x 16
nn.Conv2d(ndf * 2, ndf * 2, (1, 2), (1, 2), 0, bias=False),
nn.BatchNorm2d(ndf * 2),
nn.LeakyReLU(0.2, inplace=True),
# state size. (ndf*4) x 8 x 8
nn.Conv2d(ndf * 2, ndf * 4, (1, 4), (1, 2), 0, bias=False),
nn.BatchNorm2d(ndf * 4),
nn.LeakyReLU(0.2, inplace=True),
# state size. (ndf*4) x 8 x 8
nn.Conv2d(ndf * 4, 1, (1, 3), (1, 2), 0, bias=False),
nn.Sigmoid()
)
def forward(self, input):
output = self.main(input)
return output.view(-1, 1).squeeze(1)
netD = Discriminator().to(device)
if (device.type == 'cuda') and (ngpu > 1):
netD = nn.DataParallel(netD, list(range(ngpu)))
netD.apply(weights_init)
criterion = nn.BCELoss()
fixed_noise = torch.randn(opt.batchSize, nz, 1, 1, device=device)
real_label = 1
fake_label = 0
# setup optimizer
optimizerD = optim.Adam(netD.parameters(), lr=opt.lr, betas=(opt.beta1, 0.999))
optimizerG = optim.Adam(netG.parameters(), lr=opt.lr, betas=(opt.beta1, 0.999))
ldl = []
lgl = []
dxl = []
dgz1l = []
dgz2l = []
for epoch in range(opt.niter):
for i, data in enumerate(dataloader, 0):
data = data[2]
data.unsqueeze_(1)
data.add_(-0.5).mul_(2)
# train with real
netD.zero_grad()
real_cpu = data.to(device)
batch_size = real_cpu.size(0)
label = torch.full((batch_size,), real_label, device=device)
output = netD(real_cpu)
errD_real = criterion(output, label)
errD_real.backward()
D_x = output.mean().item()
# train with fake
noise = torch.randn(batch_size, nz, 1, 1, device=device)
fake = netG(noise)
label.fill_(fake_label)
output = netD(fake.detach())
errD_fake = criterion(output, label)
errD_fake.backward()
D_G_z1 = output.mean().item()
errD = errD_real + errD_fake
optimizerD.step()
# Update G network: maximize log(D(G(z)))
netG.zero_grad()
label.fill_(real_label) # fake labels are real for generator cost
output = netD(fake)
errG = criterion(output, label)
errG.backward()
D_G_z2 = output.mean().item()
optimizerG.step()
ldl.append(errD.item())
lgl.append(errG.item())
dxl.append(D_x)
dgz1l.append(D_G_z1)
dgz2l.append(D_G_z2)
plot_gan(ldl, lgl, dxl, dgz1l, dgz2l, opt.outf)
print('[%d/%d][%d/%d] Loss_D: %.4f Loss_G: %.4f D(x): %.4f D(G(z)): %.4f / %.4f'
% (epoch, opt.niter, i, len(dataloader),
errD.item(), errG.item(), D_x, D_G_z1, D_G_z2))
if i % 5 == 0:
vutils.save_image(real_cpu,
'%s/real_samples.png' % opt.outf,
normalize=True,pad_value=0.5)
fake = netG(fixed_noise)
vutils.save_image(fake.detach().apply_(lambda x: 1 if x > 0 else 0),
'%s/fake_samples_epoch_%03d.png' % (opt.outf, epoch),
normalize=True,pad_value=0.5)
loss = [total_val_loss, p_l2_total_loss, div_l2_total_loss, \
p_l1_total_loss, div_l1_total_loss]
filename = 'figures/fig_' + str(it) + '.png'
#if (it % 8 == 0):
# plotField(out_list, target, flags, loss, mconf, filename)
data[:, 1:3] = out_U.clone()
return data, target, loss
print('Dataset in ' + str(conf['dataDir']))
print('Plotting results at epoch ' + str(state['epoch']))
it = 0
it_8dt = 0
max_iter = 8000
data, _ = te.__getitem__(0)
data.unsqueeze_(0)
data_loss_plot = np.empty((0, 2))
fig = plt.gcf()
fig.show()
plt.legend()
plt.xlabel('Iteration')
plt.ylabel('Divergence')
fig.canvas.draw()
while (it < max_iter):
print('It = ' + str(it))
if (it % 8 == 0):
_, target = te.__getitem__(it_8dt)
target.unsqueeze_(0)
it_8dt += 1
