def getLabeledMassif(self, pattern=None):
if self._labeled_massif is None:
with self._sem_label:
if self._labeled_massif is None:
if pattern is None:
pattern = [
[1] * 3
] * 3 # [[0, 1, 0], [1, 1, 1], [0, 1, 0]]#[[1] * 3] * 3
logger.debug(
"Labeling all massifs. This takes some time !!!")
labeled_massif, self._number_massif = label(
(self.getBinnedData() > self.getBluredData()), pattern)
logger.info("Labeling found %s massifs." %
self._number_massif)
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=labeled_massif).write(
"labeled_massif_small.edf")
relabeled = utils.relabel(labeled_massif,
self.getBinnedData(),
self.getBluredData())
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(
data=relabeled).write("relabeled_massif_small.edf")
self._labeled_massif = unBinning(relabeled, self.binning,
False)
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=self._labeled_massif
).write("labeled_massif.edf")
logger.info("Labeling found %s massifs." %
self._number_massif)
return self._labeled_massif
def generate(self, N=None, batch_size=1):
K = 11
while K > 10:
clusters, N, K = generate_CRP(self.params, N=N)
data = torch.zeros([batch_size, N, 28, 28])
cumsum = np.cumsum(clusters)
for i in range(batch_size):
labels = np.random.choice(
10, size=K, replace=False
) #this is a sample from the 'base measure' for each cluster
for k in range(K):
l = labels[k]
nk = clusters[k + 1]
inds = np.random.choice(self.label_data[l].shape[0],
size=nk,
replace=False)
data[i, cumsum[k]:cumsum[k + 1], :, :] = self.label_data[l][
inds, :, :]
cs = np.empty(N, dtype=np.int32)
for k in range(K):
cs[cumsum[k]:cumsum[k + 1]] = k
arr = np.arange(N)
np.random.shuffle(arr)
cs = cs[arr]
data = data[:, arr, :, :]
cs = relabel(cs)
return data, cs, clusters, K
def watershed_center(image, center):
distance = ndi.distance_transform_edt(image)
markers, nr_blobs = ndi.label(center)
labeled = morph.watershed(-distance, markers, mask=image)
dropped, _ = ndi.label(image - (labeled > 0))
dropped = np.where(dropped > 0, dropped + nr_blobs, 0)
correct_labeled = dropped + labeled
return relabel(correct_labeled)
def drop_small(img, min_size):
freqs = itemfreq(img)
small_blob_id = freqs[freqs[:, 1] < min_size, 0]
h, w = img.shape
for i, j in product(range(h), range(w)):
if img[i, j] in small_blob_id:
img[i, j] = 0
return relabel(img)
def getLabeledMassif(self, pattern=None):
if self._labeled_massif is None:
with self._sem_label:
if self._labeled_massif is None:
if pattern is None:
pattern = [[1] * 3] * 3 # [[0, 1, 0], [1, 1, 1], [0, 1, 0]]#[[1] * 3] * 3
logger.debug("Labeling all massifs. This takes some time !!!")
labeled_massif, self._number_massif = label((self.getBinnedData() > self.getBluredData()), pattern)
logger.info("Labeling found %s massifs." % self._number_massif)
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=labeled_massif).write("labeled_massif_small.edf")
relabeled = utils.relabel(labeled_massif, self.getBinnedData(), self.getBluredData())
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=relabeled).write("relabeled_massif_small.edf")
self._labeled_massif = unBinning(relabeled, self.binning, False)
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=self._labeled_massif).write("labeled_massif.edf")
logger.info("Labeling found %s massifs." % self._number_massif)
return self._labeled_massif
def generate(self, N=None, batch_size=1):
lamb = self.params['lambda']
sigma = self.params['sigma']
x_dim = self.params['x_dim']
clusters, N, num_clusters = generate_CRP(self.params, N=N)
cumsum = np.cumsum(clusters)
data = np.empty([batch_size, N, x_dim])
cs = np.empty(N, dtype=np.int32)
for i in range(num_clusters):
mu = np.random.normal(0, lamb, size=[x_dim * batch_size, 1])
samples = np.random.normal(
mu, sigma, size=[x_dim * batch_size, clusters[i + 1]])
samples = np.swapaxes(
samples.reshape([batch_size, x_dim, clusters[i + 1]]), 1, 2)
data[:, cumsum[i]:cumsum[i + 1], :] = samples
cs[cumsum[i]:cumsum[i + 1]] = i + 1
#%shuffle the assignment order
arr = np.arange(N)
np.random.shuffle(arr)
cs = cs[arr]
data = data[:, arr, :]
# relabel cluster numbers so that they appear in order
cs = relabel(cs)
#normalize data
#means = np.expand_dims(data.mean(axis=1),1 )
medians = np.expand_dims(np.median(data, axis=1), 1)
data = data - medians
#data = 2*data/(maxs-mins)-1 #data point are now in [-1,1]
return data, cs, clusters, num_clusters
def main(args):
torch.manual_seed(args.seed)
np.random.seed(args.seed)
model = args.model
params = get_parameters(model)
params['device'] = torch.device("cuda:0" if args.cuda else "cpu")
print(params['device'])
dpmm = NeuralClustering(params).to(params['device'])
data_generator = get_generator(params)
#define containers to collect statistics
losses = [] # NLLs
accs = [] # Accuracy of the classification prediction
perm_vars = [] # permutation variance
it = 0 # iteration counter
learning_rate = 1e-4
weight_decay = 0.01
optimizer = torch.optim.Adam(dpmm.parameters(),
lr=learning_rate,
weight_decay=weight_decay)
perms = 6 # Number of permutations for each mini-batch.
# In each permutation, the order of the datapoints is shuffled.
batch_size = args.batch_size
max_it = args.iterations
if params['model'] == 'Gauss2D':
if not os.path.isdir('saved_models/Gauss2D'):
os.makedirs('saved_models/Gauss2D')
if not os.path.isdir('figures/Gauss2D'):
os.makedirs('figures/Gauss2D')
elif params['model'] == 'MNIST':
if not os.path.isdir('saved_models/MNIST'):
os.makedirs('saved_models/MNIST')
if not os.path.isdir('figures/MNIST'):
os.makedirs('figures/MNIST')
end_name = params['model']
learning_rates = {1200: 5e-5, 2200: 1e-5}
t_start = time.time()
itt = it
while True:
it += 1
if it == max_it:
break
dpmm.train()
if it % args.plot_interval == 0:
torch.cuda.empty_cache()
plot_avgs(losses,
accs,
perm_vars,
50,
save_name='./figures/train_avgs_' + end_name + '.pdf')
if params['model'] == 'Gauss2D':
fig_name = './figures/Gauss2D/samples_2D_' + str(it) + '.pdf'
print('\nCreating plot at ' + fig_name + '\n')
plot_samples_2d(dpmm,
data_generator,
N=100,
seed=it,
save_name=fig_name)
elif params['model'] == 'MNIST':
fig_name = './figures/MNIST/samples_MNIST_' + str(it) + '.pdf'
print('\nCreating plot at ' + fig_name + '\n')
plot_samples_MNIST(dpmm,
data_generator,
N=20,
seed=it,
save_name=fig_name)
if it % 100 == 0:
if 'fname' in vars():
os.remove(fname)
dpmm.params['it'] = it
fname = 'saved_models/' + end_name + '/' + end_name + '_' + str(
it) + '.pt'
torch.save(dpmm, fname)
if it in learning_rates:
optimizer = torch.optim.Adam(dpmm.parameters(),
lr=learning_rates[it],
weight_decay=weight_decay)
data, cs, clusters, K = data_generator.generate(None, batch_size)
N = data.shape[1]
loss_values = np.zeros(perms)
accuracies = np.zeros([N - 1, perms])
# The memory requirements change in each iteration according to the random values of N and K.
# If both N and K are big, an out of memory RuntimeError exception might be raised.
# When this happens, we capture the exception, reduce the batch_size to 3/4 of its value, and try again.
while True:
try:
loss = 0
for perm in range(perms):
arr = np.arange(N)
np.random.shuffle(
arr
) # permute the order in which the points are queried
cs = cs[arr]
data = data[:, arr, :]
cs = relabel(
cs
) # this makes cluster labels appear in cs[] in increasing order
this_loss = 0
dpmm.previous_n = 0
for n in range(1, N):
# points up to (n-1) are already assigned, the point n is to be assigned
logprobs = dpmm(data, cs, n)
c = cs[n]
accuracies[n - 1, perm] = np.sum(
np.argmax(logprobs.detach().to('cpu').numpy(),
axis=1) == c) / logprobs.shape[0]
this_loss -= logprobs[:, c].mean()
this_loss.backward(
) # this accumulates the gradients for each permutation
loss_values[perm] = this_loss.item() / N
loss += this_loss
perm_vars.append(loss_values.var())
losses.append(loss.item() / N)
accs.append(accuracies.mean())
optimizer.step(
) # the gradients used in this step are the sum of the gradients for each permutation
optimizer.zero_grad()
print('{0:4d} N:{1:2d} K:{2} Mean NLL:{3:.3f} Mean Acc:{4:.3f} Mean Permutation Variance: {5:.7f} Mean Time/Iteration: {6:.1f}'\
.format(it, N, K , np.mean(losses[-50:]), np.mean(accs[-50:]), np.mean(perm_vars[-50:]), (time.time()-t_start)/(it - itt) ))
break
except RuntimeError:
bsize = int(.75 * data.shape[0])
if bsize > 2:
print('RuntimeError handled ', 'N:', N, ' K:', K,
'Trying batch size:', bsize)
data = data[:bsize, :, :]
else:
break
def drop_small(img, min_size):
img = morph.remove_small_objects(img, min_size=min_size)
return relabel(img)
def main(opts, start_time=time.time()):
# taxonomy
T = np.load(
'taxonomy/{dataset}/taxonomy.npy'.format(dataset=opts.dataset)).item()
utils.update_taxonomy(opts.method, T, opts.radius, start_time)
# model
data_dim = 2048 # feature dimension before softmax
# top-down
if opts.method == 'TD':
model = models.TDModel(data_dim,
T['num_children'],
ns=opts.novel_score)
# combined
elif 'TD+' in opts.method:
TDModel = models.TDModel(data_dim,
T['num_children'],
ns=opts.novel_score,
relu=opts.test_relu,
softmax=opts.softmax)
FLModel = models.FLModel(sum(T['num_children']), len(T['wnids']))
model = nn.Sequential(TDModel, FLModel)
# flatten
else:
if opts.method == 'LOO' and opts.loo == 0.:
model = models.FLModel(data_dim, len(T['wnids_leaf']))
else:
model = models.FLModel(data_dim, len(T['wnids']))
# deep flatten
if opts.num_layers > 0:
model = nn.Sequential(
models.DeepLinearReLU([data_dim] * (opts.num_layers + 1),
no_last_relu=opts.no_last_relu), model)
if opts.gpu: model = model.cuda()
torch.backends.cudnn.benchmark = True
# optimizer and scheduler
model_parameters = FLModel.parameters(
) if 'TD+' in opts.method else model.parameters()
if opts.batch_size > 0:
optimizer = SGD(model_parameters,
lr=opts.lr,
weight_decay=opts.wd,
momentum=0.9)
scheduler = ReduceLROnPlateau(optimizer,
mode='min',
factor=opts.lr_decay,
patience=0,
verbose=False,
threshold=2e-2,
threshold_mode='rel',
cooldown=0,
min_lr=0,
eps=1e-8)
else: # full-batch
optimizer = Adam(model_parameters, lr=opts.lr, weight_decay=opts.wd)
scheduler = ReduceLROnPlateau(optimizer,
mode='min',
factor=opts.lr_decay,
patience=10,
verbose=False,
threshold=1e-4,
threshold_mode='rel',
cooldown=0,
min_lr=0,
eps=1e-8)
scheduler.cooldown_counter = opts.num_epochs // 10 # loss would increase in the first few epochs
# loss
loss_fn = models.TDLoss(
T, opts) if opts.method == 'TD' else models.LOOLoss(T, opts)
if opts.gpu: loss_fn = loss_fn.cuda()
# save path
save_path = utils.get_path(opts)
print(save_path)
# load the recent model
epoch = utils.load_model(model, optimizer, scheduler, save_path,
opts.num_epochs, start_time)
if ('TD+' in opts.method) and epoch == 0:
td_path = 'train/{dataset}/{cnn}/{method}/{td_name}' \
.format(dataset=opts.dataset, cnn=opts.cnn, method='TD', td_name=opts.td_name)
utils.load_model(TDModel, None, None, td_path, opts.num_epochs,
start_time)
prev_epoch = 0 if opts.keep else epoch
saved = True
# data loader
if opts.test: dtypes = ['train', 'val', 'known', 'novel']
else: dtypes = ['train']
if 'data_loader' in opts:
print('data_loader exists; {time:8.3f} s'.format(time=time.time() -
start_time))
data_loader = opts.data_loader
else:
data_loader = utils.get_feature_loader(dtypes, opts, start_time)
opts.data_loader = data_loader
# recover labels if relabeled previously
if 'train' in data_loader and hasattr(data_loader['train'].dataset,
'target_tensor_bak'):
data_loader['train'].dataset.target_tensor = data_loader[
'train'].dataset.target_tensor_bak
del data_loader['train'].dataset.target_tensor_bak
print('labels recovered')
# relabel
if 'RLB' in opts.method:
dataset_path = 'datasets/{dataset}'.format(dataset=opts.dataset)
relabels = utils.relabel(opts.relabel,
data_loader['train'].dataset.target_tensor, T,
opts.num_epochs, dataset_path, start_time)
data_loader['train'].dataset.target_tensor_bak = data_loader[
'train'].dataset.target_tensor
# min lr
min_lr = opts.lr * (opts.lr_decay**opts.num_lr_decay) - ee
print('{epoch:4d}/{num_epochs:4d} e; '.format(epoch=epoch,
num_epochs=opts.num_epochs),
end='')
print('start training; ', end='')
print('{time:8.3f} s'.format(time=time.time() - start_time))
for epoch in range(epoch + 1, opts.num_epochs + 1):
# stopping criterion
if optimizer.param_groups[0]['lr'] == 0.: break
# train
if 'RLB' in opts.method:
data_loader['train'].dataset.target_tensor = relabels[epoch - 1]
loss_val = train(data_loader['train'], model, loss_fn, optimizer,
epoch, T, opts, start_time)
# lr decay
if scheduler is not None:
scheduler.step(loss_val)
if optimizer.param_groups[0]['lr'] < min_lr:
optimizer.param_groups[0]['lr'] = 0.
# save model
saved = False
if opts.batch_size > 0 or epoch % opts.save_freq == 0:
utils.save_model(model, optimizer, scheduler, save_path, epoch,
opts.num_epochs, prev_epoch, start_time)
if not opts.keep: prev_epoch = epoch
saved = True
if not saved:
utils.save_model(model, optimizer, scheduler, save_path, epoch,
opts.num_epochs, prev_epoch, start_time)
print('{epoch:4d}/{num_epochs:4d} e; '.format(epoch=epoch,
num_epochs=opts.num_epochs),
end='')
print('training done; ', end='')
print('{time:8.3f} s'.format(time=time.time() - start_time))
# eval
if opts.test:
if opts.test_data_norm:
save_path += '_tdn'
if opts.method == 'TD':
ths_opt = test.val_td(data_loader, model, T, opts, save_path,
start_time)
test.test_td(ths_opt['local'], data_loader, model, T, opts,
save_path, start_time)
else:
test.test('val', data_loader, model, T, opts, save_path,
start_time)
test.test('test', data_loader, model, T, opts, save_path,
start_time)
def forward(self,data, cs, n):
# n =1,2,3..N
# elements with index below or equal to n-1 are already assigned
# element with index n is to be assigned.
# the elements from the n+1-th are not assigned
assert(n == self.previous_n+1)
self.previous_n = self.previous_n + 1
K = len(set(cs[:n])) # num of already created clusters
if n==1:
self.batch_size = data.shape[0]
self.N = data.shape[1]
assert (cs==relabel(cs)).all()
if self.params['model'] == 'Gauss2D':
# The data comes as a numpy vector
data = torch.tensor(data).float().to(self.device)
data = data.view([self.batch_size*self.N, self.params['x_dim']])
elif self.params['model'] == 'MNIST':
# The data comes as a torch tensor, we just move it to the device
data = data.to(self.device)
data = data.view([self.batch_size*self.N, 28,28])
self.hs = self.h(data).view([self.batch_size,self.N, self.h_dim])
self.Hs = torch.zeros([self.batch_size, 1, self.h_dim]).to(self.device)
self.Hs[:,0,:] = self.hs[:,0,:]
self.qs = self.q(data).view([self.batch_size,self.N, self.h_dim])
self.Q = self.qs[:,2:,].sum(dim=1) #[batch_size,h_dim]
else:
if K == self.previous_K:
self.Hs[:, cs[n-1], :] += self.hs[:,n-1,:]
else:
self.Hs = torch.cat((self.Hs,self.hs[:,n-1,:].unsqueeze(1)), dim=1)
if n==self.N-1:
self.Q = torch.zeros([self.batch_size,self.h_dim]).to(self.device) #[batch_size,h_dim]
self.previous_n = 0
else:
self.Q -= self.qs[:,n,]
self.previous_K = K
assert self.Hs.shape[1] == K
logprobs = torch.zeros([self.batch_size, K+1]).to(self.device)
# loop over the K existing clusters for datapoint n to join
for k in range(K):
Hs2 = self.Hs.clone()
Hs2[:,k,:] += self.hs[:,n,:]
Hs2 = Hs2.view([self.batch_size*K, self.h_dim])
gs = self.g(Hs2).view([self.batch_size, K, self.g_dim])
Gk = gs.sum(dim=1) #[batch_size,g_dim]
uu = torch.cat((Gk,self.Q), dim=1) #prepare argument for the call to f()
logprobs[:,k] = torch.squeeze(self.f(uu))
# consider datapoint n creating a new cluster
Hs2 = torch.cat((self.Hs,self.hs[:,n,:].unsqueeze(1)), dim=1)
Hs2 = Hs2.view([self.batch_size*(K+1), self.h_dim])
gs = self.g(Hs2).view([self.batch_size, K+1, self.g_dim])
Gk = gs.sum(dim=1)
uu = torch.cat((Gk,self.Q), dim=1) #prepare argument for the call to f()
logprobs[:,K] = torch.squeeze(self.f(uu))
# Normalize
m,_ = torch.max(logprobs,1, keepdim=True) #[batch_size,1]
logprobs = logprobs - m - torch.log( torch.exp(logprobs-m).sum(dim=1, keepdim=True))
return logprobs