def test_fluid_flat_gradcheck(bs, dim):
fluid_params = [.1, .01, .001]
defsh = tuple([bs, dim] + [res] * dim)
v = torch.randn(defsh, dtype=torch.float64, requires_grad=True).cuda()
metric = lm.FluidMetric(fluid_params)
catch_gradcheck(
f"Failed fluid flat gradcheck with batch size {bs} dim {dim}",
metric.flat, (v, ))
def test_fluid_inverse(bs, dim):
fluid_params = [.1, .01, .001]
defsh = tuple([bs, dim] + [res] * dim)
m = torch.randn(defsh, dtype=torch.float64, requires_grad=False).cuda()
metric = lm.FluidMetric(fluid_params)
v = metric.sharp(m)
vm = metric.flat(v)
assert torch.allclose(
vm, m, atol=1e-3
), f"Failed fluid inverse check with batch size {bs} dim {dim}"
def lddmm_matching(I,
J,
m=None,
lddmm_steps=1000,
lddmm_integration_steps=10,
reg_weight=1e-1,
learning_rate_pose=2e-2,
fluid_params=[1.0, .1, .01],
progress_bar=True):
"""Matching image I to J via LDDMM"""
if m is None:
defsh = [I.shape[0], 3] + list(I.shape[2:])
m = torch.zeros(defsh, dtype=I.dtype).to(I.device)
do_regridding = m.shape[2:] != I.shape[2:]
J = J.to(I.device)
matchterms = []
regterms = []
losses = []
metric = lm.FluidMetric(fluid_params)
m.requires_grad_()
pb = range(lddmm_steps)
if progress_bar: pb = tqdm(pb)
for mit in pb:
if m.grad is not None:
m.grad.detach_()
m.grad.zero_()
m.requires_grad_()
h = lm.expmap(metric, m, num_steps=lddmm_integration_steps)
if do_regridding is not None:
h = lm.regrid(h, shape=I.shape[2:], displacement=True)
Idef = lm.interp(I, h)
regterm = (metric.sharp(m) * m).mean()
matchterm = mse_loss(Idef, J)
matchterms.append(matchterm.detach().item())
regterms.append(regterm.detach().item())
loss = matchterm + reg_weight * regterm
loss.backward()
loss.detach_()
with torch.no_grad():
#v = metric.sharp(m)
#regterm = (v*m).mean()#.detach()
#del v
#losses.append(loss.detach()+ .5*reg_weight*regterm)
losses.append(loss.detach())
p = metric.flat(m.grad).detach()
if torch.isnan(losses[-1]).item():
print(f"loss is NaN at iter {mit}")
break
#if mit > 0 and losses[-1].item() > losses[-2].item():
# print(f"loss increased at iter {mit}")
#p.add_(reg_weight/np.prod(m.shape[1:]), m)
m.add_(-learning_rate_pose, p)
return m.detach(), [l.item() for l in losses], matchterms, regterms
_, I = oasis_ds_std[0]
_, J = oasis_ds_std[10]
I = I.unsqueeze(1).to('cuda')
J = J.unsqueeze(1).to(I.device)
I.requires_grad_(False)
J.requires_grad_(False)
#fluid_params=[1e-2,.0,.01]
fluid_params = [5e-2, .0, .01]
diffeo_scale = None
mmatch, losses_match = lddmm_matching(I,
J,
fluid_params=fluid_params,
diffeo_scale=diffeo_scale)
if args.plot:
sl = I.shape[3] // 2
metric = lm.FluidMetric(fluid_params)
hsmall = lm.expmap(metric, mmatch, num_steps=10)
h = hsmall
if diffeo_scale is not None:
h = lm.regrid(h, shape=I.shape[2:], displacement=True)
Idef = lm.interp(I, h)
plt.plot(losses_match, '-o')
plt.figure()
plt.subplot(1, 3, 1)
plt.imshow(I[0, 0, :, sl, :].cpu().numpy().squeeze(), cmap='gray')
plt.subplot(1, 3, 2)
plt.imshow(Idef[0, 0, :, sl, :].cpu().numpy().squeeze(), cmap='gray')
plt.subplot(1, 3, 3)
plt.imshow(J[0, 0, :, sl, :].cpu().numpy().squeeze(), cmap='gray')
plt.figure()
if diffeo_scale is None:
def test_expmap_zero(bs, dim, step, params):
defsh = tuple([bs, dim] + [res] * dim)
m = torch.zeros(defsh, dtype=torch.float64, requires_grad=False).cuda()
metric = lm.FluidMetric(params)
h = lm.expmap(metric, m, num_steps=step)
assert torch.allclose(m, h), "Failed expmap of zero is identity check"
def lddmm_atlas(dataset,
I0=None,
num_epochs=500,
batch_size=10,
lddmm_steps=1,
lddmm_integration_steps=5,
reg_weight=1e2,
learning_rate_pose = 2e2,
learning_rate_image = 1e4,
fluid_params=[0.1,0.,.01],
device='cuda',
momentum_preconditioning=True,
momentum_pattern='oasis_momenta/momentum_{}.pth',
gpu=None,
world_size=1,
rank=0):
if world_size > 1:
sampler = DistributedSampler(dataset,
num_replicas=world_size,
rank=rank)
else:
sampler = None
dataloader = DataLoader(dataset, sampler=sampler, batch_size=batch_size,
num_workers=8, pin_memory=True, shuffle=False)
if I0 is None:
# initialize base image to mean
I0 = batch_average(dataloader, dim=0)
I0 = I0.view(1,1,*I0.squeeze().shape)
#I = DenseInterp(I0)
#if gpu is not None:
#I = DistributedDataParallel(I, device_ids=[gpu], output_device=gpu)
#I = I.to(f'cuda:{gpu}')
#else:
I = I0.clone()
I = I.to(device)
#image_optimizer = torch.optim.SGD(I.parameters(),
image_optimizer = torch.optim.SGD([I],
lr=learning_rate_image,
weight_decay=0)
metric = lm.FluidMetric(fluid_params)
losses = []
reg_terms = []
iter_losses = []
epbar = range(num_epochs)
if rank == 0:
epbar = tqdm(epbar, desc='epoch')
ms = torch.zeros(len(dataset),3,*I0.shape[-3:], dtype=I0.dtype).pin_memory()
for epoch in epbar:
epoch_loss = 0.0
epoch_reg_term = 0.0
itbar = dataloader
I.requires_grad_(True)
image_optimizer.zero_grad()
for it, (ix, img) in enumerate(itbar):
m = ms[ix,...].detach()
m = m.to(device)
img = img.to(device)
for lit in range(lddmm_steps):
# compute image gradient in last step
I.requires_grad_(lit == lddmm_steps - 1)
# enables taking multiple LDDMM step per image update
m.requires_grad_(True)
if m.grad is not None:
m.grad.detach_()
m.grad.zero_()
h = lm.expmap(metric, m, num_steps=lddmm_integration_steps)
#Idef = I(h)
Idef = lm.interp(I, h)
v = metric.sharp(m)
regterm = reg_weight*(v*m).sum()
loss = (mse_loss(Idef, img, reduction='sum') + regterm) \
/ (img.numel())
loss.backward()
# this makes it so that we can reduce the loss and eventually get
# an accurate MSE for the entire dataset
with torch.no_grad():
li = (loss*(img.shape[0]/len(dataloader.dataset))).detach()
p = m.grad
if momentum_preconditioning:
p = metric.flat(p)
m.add_(-learning_rate_pose, p)
if world_size > 1:
all_reduce(li)
iter_losses.append(li.item())
m = m.detach()
del p
with torch.no_grad():
epoch_loss += li
ri = (regterm*(img.shape[0]/(img.numel()*len(dataloader.dataset)))).detach()
epoch_reg_term += ri
ms[ix,...] = m.detach().cpu()
del m, h, Idef, v, loss, regterm, img
with torch.no_grad():
if world_size > 1:
all_reduce(epoch_loss)
all_reduce(epoch_reg_term)
all_reduce(I.grad)
I.grad = I.grad/world_size
# average over iterations
I.grad = I.grad / len(dataloader)
image_optimizer.step()
losses.append(epoch_loss.item())
reg_terms.append(epoch_reg_term.item())
if rank == 0:
epbar.set_postfix(epoch_loss=epoch_loss.item(),
epoch_reg=epoch_reg_term.item())
#return I.state_dict()['I'].detach(), ms.detach(), losses, iter_losses
return I.detach(), ms.detach(), losses, iter_losses
def deep_lddmm_atlas(
dataset,
I0=None,
fluid_params=[1e-1, 0., .01],
num_epochs=500,
batch_size=2,
reg_weight=.001,
dropout=None,
closed_form_image=False,
image_update_freq=10, # how many iters between image updates
momentum_net=None,
momentum_preconditioning=True,
lddmm_integration_steps=5,
learning_rate_pose=1e-5,
learning_rate_image=1e6,
resume_checkpoint=False,
checkpoint_every=0,
checkpoint_pattern='checkpoints/{epoch}.pth',
gpu=None,
world_size=1,
rank=0):
print(locals())
from torch.utils.data import DataLoader, TensorDataset
if gpu is None:
device = 'cpu'
else:
device = f'cuda:{gpu}'
if world_size > 1:
sampler = DistributedSampler(dataset,
num_replicas=world_size,
rank=rank)
else:
sampler = None
dataloader = DataLoader(dataset,
sampler=sampler,
batch_size=batch_size,
num_workers=8,
pin_memory=True,
shuffle=False)
#I = I.clone()
if I0 is None:
# initialize base image to mean
I0 = batch_average(dataloader, dim=0)
I0 = I0.view(1, 1, *I0.squeeze().shape)
#I = DenseInterp(I0)
#if gpu is not None:
#I = DistributedDataParallel(I, device_ids=[gpu], output_device=gpu)
#I = I.to(f'cuda:{gpu}')
#else:
epoch_losses = []
iter_losses = []
if momentum_net is None:
momentum_net = MomentumPredictor(img_size=I0.shape, dropout=dropout)
momentum_net = momentum_net.to(device)
print(
f"Momentum network has {sum([p.numel() for p in momentum_net.parameters()])} parameters"
)
if world_size > 1:
momentum_net = DistributedDataParallel(momentum_net,
device_ids=[gpu],
output_device=gpu)
start_epoch = 0
if resume_checkpoint:
while True:
cpfile = checkpoint_pattern.format(epoch=start_epoch)
if not os.is_file(cpfile):
if start_epoch > 0: # load previous state
cpfile = checkpoint_pattern.format(epoch=start_epoch - 1)
I, sd = torch.load(cpfile, map_location=device)
momentum_net.load_state_dict(sd)
break
start_epoch += 1
I = I0.to(device).detach()
from torch.nn.functional import mse_loss
pose_optimizer = torch.optim.Adam(
momentum_net.parameters(),
# below we roughly compensate for scaling the loss
# the goal is to have learning rates that are independent of
# number and size of minibatches, but it's tricky to accomplish
lr=learning_rate_pose * len(dataloader),
weight_decay=1e-4)
image_optimizer = torch.optim.SGD([I],
lr=learning_rate_image,
weight_decay=0)
metric = lm.FluidMetric(fluid_params)
epbar = range(start_epoch, num_epochs)
if rank == 0:
epbar = tqdm(epbar, desc='epoch')
for epoch in epbar:
epoch_loss = 0.0
epoch_reg_term = 0.0
itbar = dataloader
if epoch > 1: # start using gradients for image after one epoch
closed_form_image = False
if closed_form_image:
splatI = torch.zeros_like(I)
splatw = torch.zeros_like(I)
splatI.requires_grad_(False)
splatw.requires_grad_(False)
if not closed_form_image and I.grad is not None:
image_optimizer.zero_grad()
I.requires_grad_(True)
for it, (ix, img) in enumerate(itbar):
pose_optimizer.zero_grad()
img = img.detach().to(I.device)
m = momentum_net(img)
if momentum_preconditioning:
m.register_hook(metric.flat)
h = lm.expmap(metric, m, num_steps=lddmm_integration_steps)
Idef = lm.interp(I, h)
v = metric.sharp(m)
reg_term = 0
if reg_weight > 0:
reg_term = reg_weight * (v * m).sum()
loss = (mse_loss(Idef, img, reduction='sum') + reg_term) \
/ (img.numel())
loss.backward()
li = (loss * (img.shape[0] / len(dataloader.dataset))).detach()
epoch_loss += li
ri = (reg_term *
(img.shape[0] /
(img.numel() * len(dataloader.dataset)))).detach()
epoch_reg_term += ri
iter_losses.append(li.item())
#itbar.set_postfix(minibatch_loss=loss.item())
pose_optimizer.step()
del loss, reg_term, v, m, h, Idef, img
with torch.no_grad():
if world_size > 1:
all_reduce(epoch_loss)
all_reduce(epoch_reg_term)
all_reduce(I.grad)
I.grad = I.grad / world_size
# average over iterations
I.grad = I.grad / len(dataloader)
image_optimizer.step()
epoch_losses.append(epoch_loss.item())
if rank == 0:
epbar.set_postfix(epoch_loss=epoch_loss.item(),
epoch_reg=epoch_reg_term.item())
return I.detach(), momentum_net, epoch_losses, iter_losses
