def _load_daae(state_dict, device=0):
"""
Load a pretrained pytorch DAAE2D state dict
:param state_dict: state dict of a daae
:param device: index of the device (if there are no GPU devices, it will be moved to the CPU)
:return: a module that corresponds to the trained network
"""
from networks.daae import DAAE2D
# extract the hyperparameters of the network
feature_maps = state_dict[
'encoder.features.convblock1.conv1.unit.0.weight'].size(0)
levels = int(list(state_dict.keys())[-15][len('decoder.features.upconv')])
bottleneck_in_features = state_dict['encoder.bottleneck.0.weight'].size(1)
bottleneck_dim = state_dict['encoder.bottleneck.0.weight'].size(0)
x = int(
np.sqrt(bottleneck_in_features * 2**(3 * levels - 1) / feature_maps))
norm = 'batch' if 'norm' in list(state_dict.keys())[2] else 'instance'
lambda_reg = 0.0
activation = 'relu'
dropout_enc = 0.0
n_hidden = state_dict['domain_classifier.linear2.unit.0.weight'].size(1)
n_domains = state_dict['domain_classifier.linear2.unit.0.weight'].size(0)
# initialize the network
net = DAAE2D(lambda_reg=lambda_reg,
input_size=[x, x],
bottleneck_dim=bottleneck_dim,
feature_maps=feature_maps,
levels=levels,
dropout_enc=dropout_enc,
norm=norm,
activation=activation,
fc_channels=(n_hidden, n_domains))
# load the parameters in the model
net.load_state_dict(state_dict)
# map to the correct device
module_to_device(net, device=device)
return net
def train_epoch(self,
loader_src,
loader_tar_ul,
loader_tar_l,
optimizer,
epoch,
augmenter=None,
print_stats=1,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader_src: source dataloader (labeled)
:param loader_tar_ul: target dataloader (unlabeled)
:param loader_tar_l: target dataloader (labeled)
:param optimizer: optimizer for the loss function
:param epoch: current epoch
:param augmenter: data augmenter
:param print_stats: frequency of printing statistics
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.train()
# keep track of the average loss during the epoch
loss_seg_src_cum = 0.0
loss_seg_tar_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# zip dataloaders
if loader_tar_l is None:
dl = zip(loader_src)
else:
dl = zip(loader_src, loader_tar_l)
# start epoch
time_start = datetime.datetime.now()
for i, data in enumerate(dl):
# transfer to suitable device
data_src = tensor_to_device(data[0], device)
if loader_tar_l is not None:
data_tar_l = tensor_to_device(data[1], device)
# augment if necessary
if loader_tar_l is None:
data_aug = (data_src[0], data_src[1])
x_src, y_src = augment_samples(data_aug, augmenter=augmenter)
else:
data_aug = (data_src[0], data_src[1])
x_src, y_src = augment_samples(data_aug, augmenter=augmenter)
data_aug = (data_tar_l[0], data_tar_l[1])
x_tar_l, y_tar_l = augment_samples(data_aug,
augmenter=augmenter)
y_tar_l = get_labels(y_tar_l, coi=self.coi, dtype=int)
# zero the gradient buffers
self.zero_grad()
# forward prop and compute loss
loss_seg_tar = torch.Tensor([0])
y_src_pred = self(x_src)
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
total_loss = loss_seg_src
if loader_tar_l is not None:
y_tar_l_pred = self(x_tar_l)
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0, ...])
total_loss = total_loss + loss_seg_tar
loss_seg_src_cum += loss_seg_src.data.cpu().numpy()
loss_seg_tar_cum += loss_seg_tar.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
# backward prop
total_loss.backward()
# apply one step in the optimization
optimizer.step()
# print statistics of necessary
if i % print_stats == 0:
print(
'[%s] Epoch %5d - Iteration %5d/%5d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, i,
len(loader_src.dataset) / loader_src.batch_size,
loss_seg_src_cum / cnt, loss_seg_tar_cum / cnt,
total_loss_cum / cnt))
# keep track of time
runtime = datetime.datetime.now() - time_start
seconds = runtime.total_seconds()
hours = seconds // 3600
minutes = (seconds - hours * 3600) // 60
seconds = seconds - hours * 3600 - minutes * 60
print_frm(
'Epoch %5d - Runtime for training: %d hours, %d minutes, %f seconds'
% (epoch, hours, minutes, seconds))
# don't forget to compute the average and print it
loss_seg_src_avg = loss_seg_src_cum / cnt
loss_seg_tar_avg = loss_seg_tar_cum / cnt
total_loss_avg = total_loss_cum / cnt
print(
'[%s] Training Epoch %4d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, loss_seg_src_avg,
loss_seg_tar_avg, total_loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars([loss_seg_src_avg, loss_seg_tar_avg, total_loss_avg], [
'train/' + s
for s in ['loss-seg-src', 'loss-seg-tar', 'total-loss']
],
writer,
epoch=epoch)
# log images if necessary
if write_images:
y_src_pred = F.softmax(y_src_pred, dim=1)[:, 1:2, :, :].data
log_images_2d(
[x_src.data, y_src.data, y_src_pred],
['train/' + s for s in ['src/x', 'src/y', 'src/y-pred']],
writer,
epoch=epoch)
if loader_tar_l is not None:
y_tar_l_pred = F.softmax(y_tar_l_pred,
dim=1)[:, 1:2, :, :].data
log_images_2d([x_tar_l.data, y_tar_l, y_tar_l_pred], [
'train/' + s
for s in ['tar/x-l', 'tar/y-l', 'tar/y-l-pred']
],
writer,
epoch=epoch)
return total_loss_avg
def test_epoch(self,
loader_src,
loader_tar_ul,
loader_tar_l,
epoch,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader_src: source dataloader (labeled)
:param loader_tar_ul: target dataloader (unlabeled)
:param loader_tar_l: target dataloader (labeled)
:param epoch: current epoch
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.eval()
# keep track of the average loss during the epoch
loss_seg_src_cum = 0.0
loss_seg_tar_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# zip dataloaders
if loader_tar_l is None:
dl = zip(loader_src)
else:
dl = zip(loader_src, loader_tar_l)
# start epoch
y_preds = []
ys = []
time_start = datetime.datetime.now()
for i, data in enumerate(dl):
# transfer to suitable device
x_src, y_src = tensor_to_device(data[0], device)
x_tar_l, y_tar_l = tensor_to_device(data[1], device)
x_src = x_src.float()
x_tar_l = x_tar_l.float()
y_src = y_src.long()
y_tar_l = y_tar_l.long()
# forward prop and compute loss
y_src_pred = self(x_src)
y_tar_l_pred = self(x_tar_l)
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0, ...])
total_loss = loss_seg_src + loss_seg_tar
loss_seg_src_cum += loss_seg_src.data.cpu().numpy()
loss_seg_tar_cum += loss_seg_tar.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
for b in range(y_tar_l_pred.size(0)):
y_preds.append(
F.softmax(y_tar_l_pred,
dim=1)[b, ...].view(y_tar_l_pred.size(1),
-1).data.cpu().numpy())
ys.append(y_tar_l[b, 0, ...].flatten().cpu().numpy())
# keep track of time
runtime = datetime.datetime.now() - time_start
seconds = runtime.total_seconds()
hours = seconds // 3600
minutes = (seconds - hours * 3600) // 60
seconds = seconds - hours * 3600 - minutes * 60
print_frm(
'Epoch %5d - Runtime for testing: %d hours, %d minutes, %f seconds'
% (epoch, hours, minutes, seconds))
# prep for metric computation
y_preds = np.concatenate(y_preds, axis=1)
ys = np.concatenate(ys)
js = np.asarray([
jaccard((ys == i).astype(int), y_preds[i, :])
for i in range(len(self.coi))
])
ams = np.asarray([
accuracy_metrics((ys == i).astype(int), y_preds[i, :])
for i in range(len(self.coi))
])
# don't forget to compute the average and print it
loss_seg_src_avg = loss_seg_src_cum / cnt
loss_seg_tar_avg = loss_seg_tar_cum / cnt
total_loss_avg = total_loss_cum / cnt
print(
'[%s] Testing Epoch %4d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, loss_seg_src_avg,
loss_seg_tar_avg, total_loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars([
loss_seg_src_avg, loss_seg_tar_avg, total_loss_avg,
np.mean(js, axis=0), *(np.mean(ams, axis=0))
], [
'test/' + s for s in [
'loss-seg-src', 'loss-seg-tar', 'total-loss', 'jaccard',
'accuracy', 'balanced-accuracy', 'precision', 'recall',
'f-score'
]
],
writer,
epoch=epoch)
# log images if necessary
if write_images:
y_src_pred = F.softmax(y_src_pred, dim=1)[:, 1:2, :, :].data
y_tar_l_pred = F.softmax(y_tar_l_pred, dim=1)[:,
1:2, :, :].data
log_images_2d([
x_src.data, y_src.data, y_src_pred, x_tar_l.data, y_tar_l,
y_tar_l_pred
], [
'test/' + s for s in [
'src/x', 'src/y', 'src/y-pred', 'tar/x-l', 'tar/y-l',
'tar/y-l-pred'
]
],
writer,
epoch=epoch)
return total_loss_avg
def test_epoch(self,
loader_src,
loader_tar_ul,
loader_tar_l,
epoch,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader_src: source dataloader (labeled)
:param loader_tar_ul: target dataloader (unlabeled)
:param loader_tar_l: target dataloader (labeled)
:param epoch: current epoch
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.eval()
# keep track of the average loss during the epoch
loss_seg_src_cum = 0.0
loss_seg_tar_cum = 0.0
loss_rec_src_cum = 0.0
loss_rec_tar_cum = 0.0
loss_dc_x_cum = 0.0
loss_dc_y_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# zip dataloaders
dl = zip(loader_src, loader_tar_ul, loader_tar_l)
# start epoch
y_preds = []
ys = []
time_start = datetime.datetime.now()
for i, data in enumerate(dl):
# transfer to suitable device
x_src, y_src = tensor_to_device(data[0], device)
x_tar_ul = tensor_to_device(data[1], device)
x_tar_l, y_tar_l = tensor_to_device(data[2], device)
x_src = x_src.float()
x_tar_ul = x_tar_ul.float()
x_tar_l = x_tar_l.float()
y_src = y_src.long()
y_tar_l = y_tar_l.long()
# get domain labels for domain confusion
dom_labels_x = tensor_to_device(
torch.zeros((x_src.size(0) + x_tar_ul.size(0))),
device).long()
dom_labels_x[x_src.size(0):] = 1
dom_labels_y = tensor_to_device(
torch.zeros((x_src.size(0) + x_tar_ul.size(0))),
device).long()
dom_labels_y[x_src.size(0):] = 1
# check train mode and compute loss
loss_seg_src = torch.Tensor([0])
loss_seg_tar = torch.Tensor([0])
loss_rec_src = torch.Tensor([0])
loss_rec_tar = torch.Tensor([0])
loss_dc_x = torch.Tensor([0])
loss_dc_y = torch.Tensor([0])
if self.train_mode == RECONSTRUCTION:
x_src_rec, x_src_rec_dom = self.forward_rec(x_src)
x_tar_ul_rec, x_tar_ul_rec_dom = self.forward_rec(x_tar_ul)
loss_rec_src = self.rec_loss(x_src_rec, x_src)
loss_rec_tar = self.rec_loss(x_tar_ul, x_tar_ul_rec)
loss_dc_x = self.dc_loss(
torch.cat((x_src_rec_dom, x_tar_ul_rec_dom), dim=0),
dom_labels_x)
total_loss = loss_rec_src + loss_rec_tar + self.lambda_dc * loss_dc_x
elif self.train_mode == SEGMENTATION:
# switch between reconstructed and original inputs
if np.random.rand() < self.p:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src)
else:
x_src_rec, _ = self.forward_rec(x_src)
y_src_pred, y_src_pred_dom = self.forward_seg(x_src_rec)
dom_labels_y[:x_src.size(0)] = 1
if np.random.rand() < self.p:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul)
else:
x_tar_ul_rec, _ = self.forward_rec(x_tar_ul)
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul_rec)
dom_labels_y[x_src.size(0):] = 1
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
loss_dc_y = self.dc_loss(
torch.cat((y_src_pred_dom, y_tar_ul_pred_dom), dim=0),
dom_labels_y)
total_loss = loss_seg_src + self.lambda_dc * loss_dc_y
y_tar_l_pred, _ = self.forward_seg(x_tar_l)
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0, ...])
total_loss = total_loss + loss_seg_tar
else:
x_src_rec, x_src_rec_dom = self.forward_rec(x_src)
if np.random.rand() < self.p:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src)
else:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src_rec)
dom_labels_y[:x_src.size(0)] = 1
x_tar_ul_rec, x_tar_ul_rec_dom = self.forward_rec(x_tar_ul)
if np.random.rand() < self.p:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul)
else:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul_rec)
dom_labels_y[x_src.size(0):] = 1
loss_rec_src = self.rec_loss(x_src_rec, x_src)
loss_rec_tar = self.rec_loss(x_tar_ul, x_tar_ul_rec)
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
loss_dc_x = self.dc_loss(
torch.cat((x_src_rec_dom, x_tar_ul_rec_dom), dim=0),
dom_labels_x)
loss_dc_y = self.dc_loss(
torch.cat((y_src_pred_dom, y_tar_ul_pred_dom), dim=0),
dom_labels_y)
total_loss = loss_seg_src + self.lambda_rec * (loss_rec_src + loss_rec_tar) + \
self.lambda_dc * (loss_dc_x + loss_dc_y)
_, y_tar_l_pred, _, y_tar_l_pred_dom = self(x_tar_l)
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0, ...])
total_loss = total_loss + loss_seg_tar
loss_seg_src_cum += loss_seg_src.data.cpu().numpy()
loss_seg_tar_cum += loss_seg_tar.data.cpu().numpy()
loss_rec_src_cum += loss_rec_src.data.cpu().numpy()
loss_rec_tar_cum += loss_rec_tar.data.cpu().numpy()
loss_dc_x_cum += loss_dc_x.data.cpu().numpy()
loss_dc_y_cum += loss_dc_y.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
if self.train_mode == SEGMENTATION or self.train_mode == JOINT:
for b in range(y_tar_l_pred.size(0)):
y_preds.append(
F.softmax(y_tar_l_pred,
dim=1)[b, ...].view(y_tar_l_pred.size(1),
-1).data.cpu().numpy())
ys.append(y_tar_l[b, 0, ...].flatten().cpu().numpy())
# keep track of time
runtime = datetime.datetime.now() - time_start
seconds = runtime.total_seconds()
hours = seconds // 3600
minutes = (seconds - hours * 3600) // 60
seconds = seconds - hours * 3600 - minutes * 60
print_frm(
'Epoch %5d - Runtime for testing: %d hours, %d minutes, %f seconds'
% (epoch, hours, minutes, seconds))
# prep for metric computation
if self.train_mode == SEGMENTATION or self.train_mode == JOINT:
y_preds = np.concatenate(y_preds, axis=1)
ys = np.concatenate(ys)
js = np.asarray([
jaccard((ys == i).astype(int), y_preds[i, :])
for i in range(len(self.coi))
])
ams = np.asarray([
accuracy_metrics((ys == i).astype(int), y_preds[i, :])
for i in range(len(self.coi))
])
# don't forget to compute the average and print it
loss_seg_src_avg = loss_seg_src_cum / cnt
loss_seg_tar_avg = loss_seg_tar_cum / cnt
loss_rec_src_avg = loss_rec_src_cum / cnt
loss_rec_tar_avg = loss_rec_tar_cum / cnt
loss_dc_x_avg = loss_dc_x_cum / cnt
loss_dc_y_avg = loss_dc_y_cum / cnt
total_loss_avg = total_loss_cum / cnt
print(
'[%s] Testing Epoch %5d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss rec src: %.6f - Loss rec tar: %.6f - Loss DCX: %.6f - Loss DCY: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, loss_seg_src_avg,
loss_seg_tar_avg, loss_rec_src_avg, loss_rec_tar_avg,
loss_dc_x_avg, loss_dc_y_avg, total_loss_avg))
# log everything
if writer is not None:
# always log scalars
if self.train_mode == RECONSTRUCTION:
log_scalars(
[loss_rec_src_avg, loss_rec_tar_avg, loss_dc_x_avg], [
'test/' + s
for s in ['loss-rec-src', 'loss-rec-tar', 'loss-dc-x']
],
writer,
epoch=epoch)
elif self.train_mode == SEGMENTATION:
log_scalars([
loss_seg_src_avg, loss_seg_tar_avg, loss_dc_y_avg,
np.mean(js, axis=0), *(np.mean(ams, axis=0))
], [
'test/' + s for s in [
'loss-seg-src', 'loss-seg-tar', 'loss-dc-y', 'jaccard',
'accuracy', 'balanced-accuracy', 'precision', 'recall',
'f-score'
]
],
writer,
epoch=epoch)
else:
log_scalars([
loss_seg_src_avg, loss_seg_tar_avg, loss_rec_src_avg,
loss_rec_tar_avg, loss_dc_x_avg, loss_dc_y_avg,
np.mean(js, axis=0), *(np.mean(ams, axis=0))
], [
'test/' + s for s in [
'loss-seg-src', 'loss-seg-tar', 'loss-rec-src',
'loss-rec-tar', 'loss-dc-x', 'loss-dc-y', 'jaccard',
'accuracy', 'balanced-accuracy', 'precision', 'recall',
'f-score'
]
],
writer,
epoch=epoch)
log_scalars([total_loss_avg],
['test/' + s for s in ['total-loss']],
writer,
epoch=epoch)
# log images if necessary
if write_images:
log_images_2d([x_src.data], ['test/' + s for s in ['src/x']],
writer,
epoch=epoch)
if self.train_mode == RECONSTRUCTION:
log_images_2d(
[x_src_rec.data, x_tar_ul.data, x_tar_ul_rec.data], [
'test/' + s
for s in ['src/x-rec', 'tar/x-ul', 'tar/x-ul-rec']
],
writer,
epoch=epoch)
elif self.train_mode == SEGMENTATION:
y_src_pred = F.softmax(y_src_pred, dim=1)[:,
1:2, :, :].data
log_images_2d(
[y_src.data, y_src_pred],
['test/' + s for s in ['src/y', 'src/y-pred']],
writer,
epoch=epoch)
if loader_tar_l is not None:
y_tar_l_pred = F.softmax(y_tar_l_pred,
dim=1)[:, 1:2, :, :].data
log_images_2d([x_tar_l.data, y_tar_l, y_tar_l_pred], [
'test/' + s
for s in ['tar/x-l', 'tar/y-l', 'tar/y-l-pred']
],
writer,
epoch=epoch)
else:
y_src_pred = F.softmax(y_src_pred, dim=1)[:,
1:2, :, :].data
log_images_2d([
x_src_rec.data, y_src.data, y_src_pred, x_tar_ul.data,
x_tar_ul_rec.data
], [
'test/' + s for s in [
'src/x-rec', 'src/y', 'src/y-pred', 'tar/x-ul',
'tar/x-ul-rec'
]
],
writer,
epoch=epoch)
if loader_tar_l is not None:
y_tar_l_pred = F.softmax(y_tar_l_pred,
dim=1)[:, 1:2, :, :].data
log_images_2d([x_tar_l.data, y_tar_l, y_tar_l_pred], [
'test/' + s
for s in ['tar/x-l', 'tar/y-l', 'tar/y-l-pred']
],
writer,
epoch=epoch)
return total_loss_avg
def train_epoch(self,
loader_src,
loader_tar_ul,
loader_tar_l,
optimizer,
epoch,
augmenter=None,
print_stats=1,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader_src: source dataloader (labeled)
:param loader_tar_ul: target dataloader (unlabeled)
:param loader_tar_l: target dataloader (labeled)
:param optimizer: optimizer for the loss function
:param epoch: current epoch
:param augmenter: data augmenter
:param print_stats: frequency of printing statistics
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.train()
# keep track of the average loss during the epoch
loss_seg_src_cum = 0.0
loss_seg_tar_cum = 0.0
loss_rec_src_cum = 0.0
loss_rec_tar_cum = 0.0
loss_dc_x_cum = 0.0
loss_dc_y_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# zip dataloaders
if loader_tar_l is None:
dl = zip(loader_src, loader_tar_ul)
else:
dl = zip(loader_src, loader_tar_ul, loader_tar_l)
# start epoch
time_start = datetime.datetime.now()
for i, data in enumerate(dl):
# transfer to suitable device
data_src = tensor_to_device(data[0], device)
x_tar_ul = tensor_to_device(data[1], device)
if loader_tar_l is not None:
data_tar_l = tensor_to_device(data[2], device)
# augment if necessary
if loader_tar_l is None:
data_aug = (data_src[0], data_src[1])
x_src, y_src = augment_samples(data_aug, augmenter=augmenter)
data_aug = (x_tar_ul, x_tar_ul)
x_tar_ul, _ = augment_samples(data_aug, augmenter=augmenter)
else:
data_aug = (data_src[0], data_src[1])
x_src, y_src = augment_samples(data_aug, augmenter=augmenter)
data_aug = (x_tar_ul, x_tar_ul)
x_tar_ul, _ = augment_samples(data_aug, augmenter=augmenter)
data_aug = (data_tar_l[0], data_tar_l[1])
x_tar_l, y_tar_l = augment_samples(data_aug,
augmenter=augmenter)
y_tar_l = get_labels(y_tar_l, coi=self.coi, dtype=int)
y_src = get_labels(y_src, coi=self.coi, dtype=int)
x_tar_ul = x_tar_ul.float()
# zero the gradient buffers
self.zero_grad()
# get domain labels for domain confusion
dom_labels_x = tensor_to_device(
torch.zeros((x_src.size(0) + x_tar_ul.size(0))),
device).long()
dom_labels_x[x_src.size(0):] = 1
dom_labels_y = tensor_to_device(
torch.zeros((x_src.size(0) + x_tar_ul.size(0))),
device).long()
dom_labels_y[x_src.size(0):] = 1
# check train mode and compute loss
loss_seg_src = torch.Tensor([0])
loss_seg_tar = torch.Tensor([0])
loss_rec_src = torch.Tensor([0])
loss_rec_tar = torch.Tensor([0])
loss_dc_x = torch.Tensor([0])
loss_dc_y = torch.Tensor([0])
if self.train_mode == RECONSTRUCTION:
x_src_rec, x_src_rec_dom = self.forward_rec(x_src)
x_tar_ul_rec, x_tar_ul_rec_dom = self.forward_rec(x_tar_ul)
loss_rec_src = self.rec_loss(x_src_rec, x_src)
loss_rec_tar = self.rec_loss(x_tar_ul, x_tar_ul_rec)
loss_dc_x = self.dc_loss(
torch.cat((x_src_rec_dom, x_tar_ul_rec_dom), dim=0),
dom_labels_x)
total_loss = loss_rec_src + loss_rec_tar + self.lambda_dc * loss_dc_x
elif self.train_mode == SEGMENTATION:
# switch between reconstructed and original inputs
if np.random.rand() < self.p:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src)
else:
x_src_rec, _ = self.forward_rec(x_src)
y_src_pred, y_src_pred_dom = self.forward_seg(x_src_rec)
dom_labels_y[:x_src.size(0)] = 1
if np.random.rand() < self.p:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul)
else:
x_tar_ul_rec, _ = self.forward_rec(x_tar_ul)
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul_rec)
dom_labels_y[x_src.size(0):] = 1
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
loss_dc_y = self.dc_loss(
torch.cat((y_src_pred_dom, y_tar_ul_pred_dom), dim=0),
dom_labels_y)
total_loss = loss_seg_src + self.lambda_dc * loss_dc_y
if loader_tar_l is not None:
y_tar_l_pred, _ = self.forward_seg(x_tar_l)
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0,
...])
total_loss = total_loss + loss_seg_tar
else:
x_src_rec, x_src_rec_dom = self.forward_rec(x_src)
if np.random.rand() < self.p:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src)
else:
y_src_pred, y_src_pred_dom = self.forward_seg(x_src_rec)
dom_labels_y[:x_src.size(0)] = 1
x_tar_ul_rec, x_tar_ul_rec_dom = self.forward_rec(x_tar_ul)
if np.random.rand() < self.p:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul)
else:
y_tar_ul_pred, y_tar_ul_pred_dom = self.forward_seg(
x_tar_ul_rec)
dom_labels_y[x_src.size(0):] = 1
loss_rec_src = self.rec_loss(x_src_rec, x_src)
loss_rec_tar = self.rec_loss(x_tar_ul, x_tar_ul_rec)
loss_seg_src = self.seg_loss(y_src_pred, y_src[:, 0, ...])
loss_dc_x = self.dc_loss(
torch.cat((x_src_rec_dom, x_tar_ul_rec_dom), dim=0),
dom_labels_x)
loss_dc_y = self.dc_loss(
torch.cat((y_src_pred_dom, y_tar_ul_pred_dom), dim=0),
dom_labels_y)
total_loss = loss_seg_src + self.lambda_rec * (loss_rec_src + loss_rec_tar) + \
self.lambda_dc * (loss_dc_x + loss_dc_y)
if loader_tar_l is not None:
_, y_tar_l_pred, _, y_tar_l_pred_dom = self(x_tar_l)
loss_seg_tar = self.seg_loss(y_tar_l_pred, y_tar_l[:, 0,
...])
total_loss = total_loss + loss_seg_tar
loss_seg_src_cum += loss_seg_src.data.cpu().numpy()
loss_seg_tar_cum += loss_seg_tar.data.cpu().numpy()
loss_rec_src_cum += loss_rec_src.data.cpu().numpy()
loss_rec_tar_cum += loss_rec_tar.data.cpu().numpy()
loss_dc_x_cum += loss_dc_x.data.cpu().numpy()
loss_dc_y_cum += loss_dc_y.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
# backward prop
total_loss.backward()
# apply one step in the optimization
optimizer.step()
# print statistics of necessary
if i % print_stats == 0:
print(
'[%s] Epoch %5d - Iteration %5d/%5d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss rec src: %.6f - Loss rec tar: %.6f - Loss DCX: %.6f - Loss DCY: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, i,
len(loader_src.dataset) / loader_src.batch_size,
loss_seg_src_cum / cnt, loss_seg_tar_cum / cnt,
loss_rec_src_cum / cnt, loss_rec_tar_cum / cnt,
loss_dc_x_cum / cnt, loss_dc_y_cum / cnt,
total_loss_cum / cnt))
# keep track of time
runtime = datetime.datetime.now() - time_start
seconds = runtime.total_seconds()
hours = seconds // 3600
minutes = (seconds - hours * 3600) // 60
seconds = seconds - hours * 3600 - minutes * 60
print_frm(
'Epoch %5d - Runtime for training: %d hours, %d minutes, %f seconds'
% (epoch, hours, minutes, seconds))
# don't forget to compute the average and print it
loss_seg_src_avg = loss_seg_src_cum / cnt
loss_seg_tar_avg = loss_seg_tar_cum / cnt
loss_rec_src_avg = loss_rec_src_cum / cnt
loss_rec_tar_avg = loss_rec_tar_cum / cnt
loss_dc_x_avg = loss_dc_x_cum / cnt
loss_dc_y_avg = loss_dc_y_cum / cnt
total_loss_avg = total_loss_cum / cnt
print(
'[%s] Training Epoch %4d - Loss seg src: %.6f - Loss seg tar: %.6f - Loss rec src: %.6f - Loss rec tar: %.6f - Loss DCX: %.6f - Loss DCY: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, loss_seg_src_avg,
loss_seg_tar_avg, loss_rec_src_avg, loss_rec_tar_avg,
loss_dc_x_avg, loss_dc_y_avg, total_loss_avg))
# log everything
if writer is not None:
# always log scalars
if self.train_mode == RECONSTRUCTION:
log_scalars(
[loss_rec_src_avg, loss_rec_tar_avg, loss_dc_x_avg], [
'train/' + s
for s in ['loss-rec-src', 'loss-rec-tar', 'loss-dc-x']
],
writer,
epoch=epoch)
elif self.train_mode == SEGMENTATION:
log_scalars(
[loss_seg_src_avg, loss_seg_tar_avg, loss_dc_y_avg], [
'train/' + s
for s in ['loss-seg-src', 'loss-seg-tar', 'loss-dc-y']
],
writer,
epoch=epoch)
else:
log_scalars([
loss_seg_src_avg, loss_seg_tar_avg, loss_rec_src_avg,
loss_rec_tar_avg, loss_dc_x_avg, loss_dc_y_avg
], [
'train/' + s for s in [
'loss-seg-src', 'loss-seg-tar', 'loss-rec-src',
'loss-rec-tar', 'loss-dc-x', 'loss-dc-y'
]
],
writer,
epoch=epoch)
log_scalars([total_loss_avg],
['train/' + s for s in ['total-loss']],
writer,
epoch=epoch)
# log images if necessary
if write_images:
log_images_2d([x_src.data], ['train/' + s for s in ['src/x']],
writer,
epoch=epoch)
if self.train_mode == RECONSTRUCTION:
log_images_2d(
[x_src_rec.data, x_tar_ul.data, x_tar_ul_rec.data], [
'train/' + s
for s in ['src/x-rec', 'tar/x-ul', 'tar/x-ul-rec']
],
writer,
epoch=epoch)
elif self.train_mode == SEGMENTATION:
y_src_pred = F.softmax(y_src_pred, dim=1)[:,
1:2, :, :].data
log_images_2d(
[y_src.data, y_src_pred],
['train/' + s for s in ['src/y', 'src/y-pred']],
writer,
epoch=epoch)
if loader_tar_l is not None:
y_tar_l_pred = F.softmax(y_tar_l_pred,
dim=1)[:, 1:2, :, :].data
log_images_2d([x_tar_l.data, y_tar_l, y_tar_l_pred], [
'train/' + s
for s in ['tar/x-l', 'tar/y-l', 'tar/y-l-pred']
],
writer,
epoch=epoch)
else:
y_src_pred = F.softmax(y_src_pred, dim=1)[:,
1:2, :, :].data
log_images_2d([
x_src_rec.data, y_src.data, y_src_pred, x_tar_ul.data,
x_tar_ul_rec.data
], [
'train/' + s for s in [
'src/x-rec', 'src/y', 'src/y-pred', 'tar/x-ul',
'tar/x-ul-rec'
]
],
writer,
epoch=epoch)
if loader_tar_l is not None:
y_tar_l_pred = F.softmax(y_tar_l_pred,
dim=1)[:, 1:2, :, :].data
log_images_2d([x_tar_l.data, y_tar_l, y_tar_l_pred], [
'train/' + s
for s in ['tar/x-l', 'tar/y-l', 'tar/y-l-pred']
],
writer,
epoch=epoch)
return total_loss_avg
def test_epoch(self,
loader_src,
loader_tar,
loss_seg_fn,
loss_rec_fn,
epoch,
writer=None,
write_images=False,
device=0):
"""
Tests the network for one epoch
:param loader_src: source dataloader (should be labeled)
:param loader_tar: target dataloader (should be labeled)
:param loss_seg_fn: segmentation loss function
:param loss_rec_fn: reconstruction loss function
:param epoch: current epoch
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.eval()
# keep track of the average loss and metrics during the epoch
loss_seg_cum = 0.0
loss_rec_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# start epoch
y_src_preds = []
ys_src = []
y_tar_preds = []
ys_tar = []
for i, data in enumerate(zip(loader_src, loader_tar)):
# get inputs and transfer to suitable device
x_src, y_src = tensor_to_device(data[0], device)
x_tar, y_tar = tensor_to_device(data[1], device)
y_src = get_labels(y_src, coi=self.coi, dtype=int)
y_tar = get_labels(y_tar, coi=self.coi, dtype=int)
x_src = x_src.float()
x_tar = x_tar.float()
# zero the gradient buffers
self.zero_grad()
# forward prop
y_src_pred = self(x_src)
x_src_pred = self.reconstruction_outputs
y_tar_pred = self(x_tar)
x_tar_pred = self.reconstruction_outputs
# compute loss
loss_seg = loss_seg_fn(y_src_pred, y_src)
loss_rec = 0.5 * (loss_rec_fn(x_src_pred, x_src) +
loss_rec_fn(x_tar_pred, x_tar))
total_loss = loss_seg + self.lambda_rec * loss_rec
loss_seg_cum += loss_seg.data.cpu().numpy()
loss_rec_cum += loss_rec.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
for b in range(y_src_pred.size(0)):
y_src_preds.append(
F.softmax(y_src_pred, dim=1).data.cpu().numpy()[b, 1, ...])
y_tar_preds.append(
F.softmax(y_tar_pred, dim=1).data.cpu().numpy()[b, 1, ...])
ys_src.append(y_src[b, 0, ...].cpu().numpy())
ys_tar.append(y_tar[b, 0, ...].cpu().numpy())
# compute interesting metrics
y_src_preds = np.asarray(y_src_preds)
y_tar_preds = np.asarray(y_tar_preds)
ys_src = np.asarray(ys_src)
ys_tar = np.asarray(ys_tar)
j_src = jaccard(ys_src, y_src_preds)
j_tar = jaccard(ys_src, y_tar_preds)
a_src, ba_src, p_src, r_src, f_src = accuracy_metrics(
ys_src, y_src_preds)
a_tar, ba_tar, p_tar, r_tar, f_tar = accuracy_metrics(
ys_tar, y_tar_preds)
# don't forget to compute the average and print it
loss_seg_avg = loss_seg_cum / cnt
loss_rec_avg = loss_rec_cum / cnt
total_loss_avg = total_loss_cum / cnt
print('[%s] Epoch %5d - Loss seg: %.6f - Loss rec: %.6f - Loss: %.6f' %
(datetime.datetime.now(), epoch, loss_seg_avg, loss_rec_avg,
total_loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars([
loss_seg_avg, loss_rec_avg, total_loss_avg, j_src, a_src,
ba_src, p_src, r_src, f_src, j_tar, a_tar, ba_tar, p_tar,
r_tar, f_tar
], [
'test/' + s for s in [
'loss-rec', 'loss-seg', 'total-loss', 'src/jaccard',
'src/accuracy', 'src/balanced-accuracy', 'src/precision',
'src/recall', 'src/f-score', 'tar/jaccard', 'tar/accuracy',
'tar/balanced-accuracy', 'tar/precision', 'tar/recall',
'tar/f-score'
]
],
writer,
epoch=epoch)
# log images if necessary
if write_images:
y_src_pred = F.softmax(y_src_pred, dim=1)[:, 1:2, ...].data
y_tar_pred = F.softmax(y_tar_pred, dim=1)[:, 1:2, ...].data
log_images_3d([
x_src, x_src_pred.data, y_src, y_src_pred, x_tar,
x_tar_pred.data, y_tar, y_tar_pred
], [
'test/' + s for s in [
'src/x', 'src/x-pred', 'src/y', 'src/y-pred', 'tar/x',
'tar/x-pred', 'tar/y', 'tar/y-pred'
]
],
writer,
epoch=epoch)
return total_loss_avg
def train_epoch_semi_supervised(self,
loader_src,
loader_tar_ul,
loader_tar_l,
loss_seg_fn,
loss_rec_fn,
optimizer,
epoch,
augmenter_src=None,
augmenter_tar=None,
print_stats=1,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader_src: source dataloader (labeled)
:param loader_tar_ul: target dataloader (unlabeled)
:param loader_tar_l: target dataloader (labeled)
:param loss_seg_fn: segmentation loss function
:param loss_rec_fn: reconstruction loss function
:param optimizer: optimizer for the loss function
:param epoch: current epoch
:param augmenter_src: source data augmenter
:param augmenter_tar: target data augmenter
:param print_stats: frequency of printing statistics
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# perform training on GPU/CPU
module_to_device(self, device)
self.train()
# keep track of the average loss during the epoch
loss_seg_cum = 0.0
loss_rec_cum = 0.0
total_loss_cum = 0.0
cnt = 0
# start epoch
for i, data in enumerate(zip(loader_src, loader_tar_ul, loader_tar_l)):
# transfer to suitable device
data_src = tensor_to_device(data[0], device)
x_tar_ul = tensor_to_device(data[1], device)
data_tar_l = tensor_to_device(data[2], device)
# augment if necessary
x_src, y_src = augment_samples(data_src, augmenter=augmenter_src)
x_tar_l, y_tar_l = augment_samples(data_tar_l,
augmenter=augmenter_tar)
y_src = get_labels(y_src, coi=self.coi, dtype=int)
y_tar_l = get_labels(y_tar_l, coi=self.coi, dtype=int)
x_tar_ul = x_tar_ul.float()
# zero the gradient buffers
self.zero_grad()
# forward prop
y_src_pred = self(x_src)
x_src_pred = self.reconstruction_outputs
y_tar_ul_pred = self(x_tar_ul)
x_tar_ul_pred = self.reconstruction_outputs
y_tar_l_pred = self(x_tar_l)
x_tar_l_pred = self.reconstruction_outputs
# compute loss
loss_seg = 0.5 * (loss_seg_fn(y_src_pred, y_src) +
loss_seg_fn(y_tar_l_pred, y_tar_l))
loss_rec = 0.5 * (loss_rec_fn(x_src_pred, x_src) +
loss_rec_fn(x_tar_ul_pred, x_tar_ul))
total_loss = loss_seg + self.lambda_rec * loss_rec
loss_seg_cum += loss_seg.data.cpu().numpy()
loss_rec_cum += loss_rec.data.cpu().numpy()
total_loss_cum += total_loss.data.cpu().numpy()
cnt += 1
# backward prop
total_loss.backward()
# apply one step in the optimization
optimizer.step()
# print statistics of necessary
if i % print_stats == 0:
print(
'[%s] Epoch %5d - Iteration %5d/%5d - Loss seg: %.6f - Loss rec: %.6f - Loss: %.6f'
% (datetime.datetime.now(), epoch, i,
len(loader_src.dataset) / loader_src.batch_size,
loss_seg, loss_rec, total_loss))
# don't forget to compute the average and print it
loss_seg_avg = loss_seg_cum / cnt
loss_rec_avg = loss_rec_cum / cnt
total_loss_avg = total_loss_cum / cnt
print('[%s] Epoch %5d - Loss seg: %.6f - Loss rec: %.6f - Loss: %.6f' %
(datetime.datetime.now(), epoch, loss_seg_avg, loss_rec_avg,
total_loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars(
[loss_seg_avg, loss_rec_avg, total_loss_avg],
['train/' + s for s in ['loss-rec', 'loss-seg', 'total-loss']],
writer,
epoch=epoch)
# log images if necessary
if write_images:
y_src_pred = F.softmax(y_src_pred, dim=1)[:, 1:2, ...].data
y_tar_l_pred = F.softmax(y_tar_l_pred, dim=1)[:, 1:2, ...].data
log_images_3d([
x_src, x_src_pred.data, y_src, y_src_pred, x_tar_l,
x_tar_l_pred.data, y_tar_l, y_tar_l_pred
], [
'train/' + s for s in [
'src/x', 'src/x-pred', 'src/y', 'src/y-pred', 'tar/x',
'tar/x-pred', 'tar/y', 'tar/y-pred'
]
],
writer,
epoch=epoch)
return total_loss_avg
def test_epoch(self,
loader,
loss_rec_fn,
loss_kl_fn,
epoch,
writer=None,
write_images=False,
device=0):
"""
Tests the network for one epoch
:param loader: dataloader
:param loss_rec_fn: reconstruction loss function
:param loss_kl_fn: kullback leibler loss function
:param epoch: current epoch
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average testing loss over the epoch
"""
# make sure network is on the gpu and in training mode
module_to_device(self, device)
self.eval()
# keep track of the average losses during the epoch
loss_rec_cum = 0.0
loss_kl_cum = 0.0
loss_cum = 0.0
cnt = 0
# start epoch
z = []
li = []
for i, data in enumerate(loader):
# transfer to suitable device
x = tensor_to_device(data.float(), device)
# forward prop
x_pred = torch.sigmoid(self(x))
z.append(_reparametrise(self.mu, self.logvar).cpu().data.numpy())
li.append(x.cpu().data.numpy())
# compute loss
loss_rec = loss_rec_fn(x_pred, x)
loss_kl = loss_kl_fn(self.mu, self.logvar)
loss = loss_rec + self.beta * loss_kl
loss_rec_cum += loss_rec.data.cpu().numpy()
loss_kl_cum += loss_kl.data.cpu().numpy()
loss_cum += loss.data.cpu().numpy()
cnt += 1
# don't forget to compute the average and print it
loss_rec_avg = loss_rec_cum / cnt
loss_kl_avg = loss_kl_cum / cnt
loss_avg = loss_cum / cnt
print_frm(
'Epoch %5d - Average test loss rec: %.6f - Average test loss KL: %.6f - Average test loss: %.6f'
% (epoch, loss_rec_avg, loss_kl_avg, loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars([loss_rec_avg, loss_kl_avg, loss_avg],
['test/' + s for s in ['loss-rec', 'loss-kl', 'loss']],
writer,
epoch=epoch)
# log images if necessary
if write_images:
log_images_2d([x, x_pred],
['test/' + s for s in ['x', 'x_pred']],
writer,
epoch=epoch)
return loss_avg
def train_epoch(self,
loader,
loss_rec_fn,
loss_kl_fn,
optimizer,
epoch,
augmenter=None,
print_stats=1,
writer=None,
write_images=False,
device=0):
"""
Trains the network for one epoch
:param loader: dataloader
:param loss_rec_fn: reconstruction loss function
:param loss_kl_fn: kullback leibler loss function
:param optimizer: optimizer for the loss function
:param epoch: current epoch
:param augmenter: data augmenter
:param print_stats: frequency of printing statistics
:param writer: summary writer
:param write_images: frequency of writing images
:param device: GPU device where the computations should occur
:return: average training loss over the epoch
"""
# make sure network is on the gpu and in training mode
module_to_device(self, device)
self.train()
# keep track of the average losses during the epoch
loss_rec_cum = 0.0
loss_kl_cum = 0.0
loss_cum = 0.0
cnt = 0
# start epoch
for i, data in enumerate(loader):
# transfer to suitable device
x = tensor_to_device(data.float(), device)
# get the inputs and augment if necessary
if augmenter is not None:
x = augmenter(x)
# zero the gradient buffers
self.zero_grad()
# forward prop
x_pred = torch.sigmoid(self(x))
# compute loss
loss_rec = loss_rec_fn(x_pred, x)
loss_kl = loss_kl_fn(self.mu, self.logvar)
loss = loss_rec + self.beta * loss_kl
loss_rec_cum += loss_rec.data.cpu().numpy()
loss_kl_cum += loss_kl.data.cpu().numpy()
loss_cum += loss.data.cpu().numpy()
cnt += 1
# backward prop
loss.backward()
# apply one step in the optimization
optimizer.step()
# print statistics if necessary
if i % print_stats == 0:
print_frm(
'Epoch %5d - Iteration %5d/%5d - Loss Rec: %.6f - Loss KL: %.6f - Loss: %.6f'
% (epoch, i, len(loader.dataset) / loader.batch_size,
loss_rec, loss_kl, loss))
# don't forget to compute the average and print it
loss_rec_avg = loss_rec_cum / cnt
loss_kl_avg = loss_kl_cum / cnt
loss_avg = loss_cum / cnt
print_frm(
'Epoch %5d - Average train loss rec: %.6f - Average train loss KL: %.6f - Average train loss: %.6f'
% (epoch, loss_rec_avg, loss_kl_avg, loss_avg))
# log everything
if writer is not None:
# always log scalars
log_scalars(
[loss_rec_avg, loss_kl_avg, loss_avg],
['train/' + s for s in ['loss-rec', 'loss-kl', 'loss']],
writer,
epoch=epoch)
# log images if necessary
if write_images:
log_images_2d([x, x_pred],
['train/' + s for s in ['x', 'x_pred']],
writer,
epoch=epoch)
return loss_avg
def segment_multichannel_3d(data,
net,
input_shape,
in_channels=1,
batch_size=1,
step_size=None,
train=False,
track_progress=False,
device=0,
orientation=0,
normalization='unit'):
"""
Segment a multichannel 3D image using a specific network
:param data: 4D array (C, Z, Y, X) representing the multichannel 3D image
:param net: image-to-image segmentation network
:param input_shape: size of the inputs (either 2 or 3-tuple)
:param in_channels: amount of subsequent slices that serve as input for the network (should be odd)
:param batch_size: batch size for processing
:param step_size: step size of the sliding window
:param train: evaluate the network in training mode
:param track_progress: optionally, for tracking progress with progress bar
:param device: GPU device where the computations should occur
:param orientation: orientation to perform segmentation: 0-Z, 1-Y, 2-X (only for 2D based segmentation)
:param normalization: type of data normalization (unit, z or minmax)
:return: the segmented image
"""
# make sure we compute everything on the correct device
module_to_device(net, device)
# set the network in the correct mode
if train:
net.train()
else:
net.eval()
# orient data if necessary
data = _orient(data, orientation)
# pad data if necessary
data, pad_width = _pad(data, input_shape, in_channels)
# 2D or 3D
is2d = len(input_shape) == 2
# get the amount of channels
channels = data.shape[0]
if is2d:
channels = in_channels
# initialize the step size
step_size = _init_step_size(step_size, input_shape, is2d)
# gaussian window for smooth block merging
g_window = _init_gaussian_window(input_shape, is2d)
# allocate space
seg_cum = np.zeros((net.out_channels, *data.shape[1:]))
counts_cum = np.zeros(data.shape[1:])
# define sliding window
sw = _init_sliding_window(data, step_size, input_shape, in_channels, is2d,
track_progress, normalization)
# start prediction
batch_counter = 0
batch = np.zeros((batch_size, channels, *input_shape))
positions = np.zeros((batch_size, 3), dtype=int)
for (z, y, x, inputs) in sw:
# fill batch
batch[batch_counter, ...] = inputs
positions[batch_counter, :] = [z, y, x]
# increment batch counter
batch_counter += 1
# perform segmentation when a full batch is filled
if batch_counter == batch_size:
# process a single batch
_process_batch(net, batch, device, seg_cum, counts_cum, g_window,
positions, batch_size, input_shape, in_channels,
is2d)
# reset batch counter
batch_counter = 0
# don't forget to process the last batch
_process_batch(net, batch, device, seg_cum, counts_cum, g_window,
positions, batch_size, input_shape, in_channels, is2d)
# crop out the symmetric extension and compute segmentation
data, seg_cum, counts_cum = _crop(data, seg_cum, counts_cum, pad_width)
for c in range(net.out_channels):
seg_cum[c, ...] = np.divide(seg_cum[c, ...], counts_cum)
# reorient data to its original orientation
data = _orient(data, orientation)
seg_cum = _orient(seg_cum, orientation)
return seg_cum
def segment_multichannel_2d(data,
net,
input_shape,
batch_size=1,
step_size=None,
train=False,
track_progress=False,
device=0,
normalization='unit'):
"""
Segment a multichannel 2D image using a specific network
:param data: 3D array (C, Y, X) representing the multichannel 2D image
:param net: image-to-image segmentation network
:param input_shape: size of the inputs (2-tuple)
:param batch_size: batch size for processing
:param step_size: step size of the sliding window
:param train: evaluate the network in training mode
:param track_progress: optionally, for tracking progress with progress bar
:param device: GPU device where the computations should occur
:param normalization: type of data normalization (unit, z or minmax)
:return: the segmented image
"""
# make sure we compute everything on the correct device
module_to_device(net, device)
# set the network in the correct mode
if train:
net.train()
else:
net.eval()
# pad data if necessary
data, pad_width = _pad(data[:, np.newaxis, ...], input_shape, 1)
data = data[:, 0, ...]
# get the amount of channels
channels = data.shape[0]
# initialize the step size
step_size = _init_step_size(step_size, input_shape, True)
# gaussian window for smooth block merging
g_window = _init_gaussian_window(input_shape, True)
# allocate space
seg_cum = np.zeros((net.out_channels, 1, *data.shape[1:]))
counts_cum = np.zeros((1, *data.shape[1:]))
# define sliding window
sw = _init_sliding_window(data[np.newaxis, ...],
[channels, *step_size[1:]], input_shape,
channels, True, track_progress, normalization)
# start prediction
batch_counter = 0
batch = np.zeros((batch_size, channels, *input_shape))
positions = np.zeros((batch_size, 3), dtype=int)
for (z, y, x, inputs) in sw:
# fill batch
batch[batch_counter, ...] = inputs
positions[batch_counter, :] = [z, y, x]
# increment batch counter
batch_counter += 1
# perform segmentation when a full batch is filled
if batch_counter == batch_size:
# process a single batch
_process_batch(net, batch, device, seg_cum, counts_cum, g_window,
positions, batch_size, input_shape, 1, True)
# reset batch counter
batch_counter = 0
# don't forget to process the last batch
_process_batch(net, batch, device, seg_cum, counts_cum, g_window,
positions, batch_size, input_shape, 1, True)
# crop out the symmetric extension and compute segmentation
data, seg_cum, counts_cum = _crop(data[:, np.newaxis, ...], seg_cum,
counts_cum, pad_width)
for c in range(net.out_channels):
seg_cum[c, ...] = np.divide(seg_cum[c, ...], counts_cum)
seg_cum = seg_cum[:, 0, ...]
return seg_cum
