def generate_raw(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
fn = '/'.join([self.exec_dir(), 'raw'])
with open(fn, 'w') as f:
f.write('''<vddb>
<query>
<return_code>0</return_code>
<extra_info>Success</extra_info>
</query>
<matches size="%s" status="0">''' %
(len(self.result['matches']), ))
for m in self.result['matches']:
t = 'audio' if m['video_duration'] == 0 else 'video'
f.write(
'''<match>
<master_uuid>%s</master_uuid>
<master_name>%s</master_name>
<instance_id>%s</instance_id>
<instance_name>%s</instance_name>
<track_type>%s</track_type>
<track_id>%s</track_id>
<match_duration>%s</match_duration>
<score>%s</score>
<reference_offset>%s</reference_offset>
<sample_offset>%s</sample_offset>
</match>''' %
(str(m['meta_uuid']), m['meta_name'].encode('utf-8'),
str(m['instance_id']), m['instance_name'].encode('utf-8'),
str(m['match_type']), str(m['track_id']),
str(m[t + '_duration']), str(m[t + '_score']),
str(m[t + '_ref_offset']), str(m[t + '_sample_offset'])))
f.write(''' </matches>
</vddb>''')
def generate_raw(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
fn = '/'.join([self.exec_dir(), 'raw'])
with open(fn, 'w') as f:
f.write('''<vddb>
<query>
<return_code>0</return_code>
<extra_info>Success</extra_info>
</query>
<matches size="%s" status="0">'''
% (len(self.result['matches']),))
for m in self.result['matches']:
t = 'audio' if m['video_duration'] == 0 else 'video'
f.write('''<match>
<master_uuid>%s</master_uuid>
<master_name>%s</master_name>
<instance_id>%s</instance_id>
<instance_name>%s</instance_name>
<track_type>%s</track_type>
<track_id>%s</track_id>
<match_duration>%s</match_duration>
<score>%s</score>
<reference_offset>%s</reference_offset>
<sample_offset>%s</sample_offset>
</match>''' % (str(m['meta_uuid']), m['meta_name'].encode('utf-8'),
str(m['instance_id']), m['instance_name'].encode('utf-8'),
str(m['match_type']), str(m['track_id']),
str(m[t + '_duration']), str(m[t + '_score']),
str(m[t + '_ref_offset']),
str(m[t + '_sample_offset'])))
f.write(''' </matches>
</vddb>''')
def query_dir(self, backend):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
task_dir = '/'.join([self.path, 'var', 'tmp', ds, uuid])
return '/'.join([task_dir, backend, self.timestr] +
(['hot'] if self.state.hot else []) +
(['slicing'] if self.state.slicing else []))
def query_dir(self, backend):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
task_dir = '/'.join([self.path, 'var', 'tmp', ds, uuid])
return '/'.join([task_dir, backend, self.timestr] +
(['hot'] if self.state.hot else []) +
(['slicing'] if self.state.slicing else []))
def dna_file(self):
if self.state.slicing:
ds = datestr(self.task.created_at)
uuid = self.task.uuid
task_dir = '/'.join([self.path, 'var', 'tmp', ds, uuid])
# all backends can share the same sliced dna
return '/'.join([task_dir, self.timestr, 'sliced.dna'])
else:
return self.dna
def dna_file(self):
if self.state.slicing:
ds = datestr(self.task.created_at)
uuid = self.task.uuid
task_dir = '/'.join([self.path, 'var', 'tmp', ds, uuid])
# all backends can share the same sliced dna
return '/'.join([task_dir, self.timestr, 'sliced.dna'])
else:
return self.dna
def __init__(self, task, account, backend, site_file, timestr):
self.path = getenv('MW_HOME')
assert self.path != None
self.logger = logging.getLogger('mwtm_query')
self.task = task
self.account = account
self.backend = backend
# self.parse_extra(backend.extra)
self.site_file = site_file
self.timestr = timestr
ds = datestr(self.task.created_at)
uuid = self.task.uuid
self.dna = '/'.join([self.path, 'var', 'tmp', ds, uuid, timestr, 'merge.dna'])
self.scope = None
self.state = None
self.result = {}
def __init__(self, task, account, backend, site_file, timestr):
self.path = getenv('MW_HOME')
assert self.path != None
self.logger = logging.getLogger('mwtm_query')
self.task = task
self.account = account
self.backend = backend
# self.parse_extra(backend.extra)
self.site_file = site_file
self.timestr = timestr
ds = datestr(self.task.created_at)
uuid = self.task.uuid
self.dna = '/'.join(
[self.path, 'var', 'tmp', ds, uuid, timestr, 'merge.dna'])
self.scope = None
self.state = None
self.result = {}
def task_dir(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
return '/'.join([self.path, 'var', 'cache', ds, uuid[6:8], uuid[21:23],
uuid])
def exec_dir(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
return '/'.join([self.path, 'var', 'tmp', ds, uuid, self.timestr])
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--batchSz', type=int, default=5)
parser.add_argument('--dice', action='store_true', default=True)
parser.add_argument('--nEpochs', type=int, default=600)
parser.add_argument('--inChannels', type=int, default=2)
parser.add_argument('--start-epoch',
default=0,
type=int,
metavar='N',
help='manual epoch number (useful on restarts)')
parser.add_argument('--resume',
default='',
type=str,
metavar='PATH',
help='path to latest checkpoint (default: none)')
parser.add_argument('--fold_id',
default='1',
type=str,
help='Select subject for fold validation')
parser.add_argument('--weight-decay',
'--wd',
default=1e-8,
type=float,
metavar='W',
help='weight decay (default: 1e-8)')
parser.add_argument('--lr',
default=1e-3,
type=float,
help='learning rate (default: 1e-3)')
parser.add_argument('--cuda', action='store_true', default=True)
parser.add_argument('--save')
parser.add_argument('--model',
type=str,
default='UNET3D',
choices=('VNET', 'VNET2', 'UNET3D', 'DENSENET1',
'DENSENET2', 'DENSENET3', 'HYPERDENSENET'))
parser.add_argument('--opt',
type=str,
default='sgd',
choices=('sgd', 'adam', 'rmsprop'))
args = parser.parse_args()
best_prec1 = 100.
DIM = (128, 128, 32)
training_generator, val_generator = generate_datasets(DIM,
fold_id=args.fold_id,
samples_train=500,
samples_val=10)
args.cuda = args.cuda and torch.cuda.is_available()
torch.manual_seed(1777777)
if args.cuda:
torch.cuda.manual_seed(1777777)
args.save = args.model + '_checkpoints/' + args.model + '_base_{}_fold_id_{}'.format(
utils.datestr(), args.fold_id)
if os.path.exists(args.save):
shutil.rmtree(args.save)
os.mkdir(args.save)
else:
os.makedirs(args.save)
weight_decay = args.weight_decay
print("Building Model . . . . . . . .")
if args.model == 'VNET2':
model = medical_zoo.VNetLight(elu=False, nll=False)
elif (args.model == 'UNET3D'):
model = medical_zoo.UNet3D(in_channels=2, n_classes=4)
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
best_prec1 = checkpoint['best_prec1']
model.load_state_dict(checkpoint['state_dict'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.evaluate, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
print('Number of params: {}'.format(
sum([p.data.nelement() for p in model.parameters()])))
if args.opt == 'sgd':
optimizer = optim.SGD(model.parameters(),
lr=args.lr,
momentum=0.5,
weight_decay=weight_decay)
elif args.opt == 'adam':
optimizer = optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=weight_decay)
elif args.opt == 'rmsprop':
optimizer = optim.RMSprop(model.parameters(),
lr=args.lr,
weight_decay=weight_decay)
train_f = open(os.path.join(args.save, 'train.csv'), 'w')
val_f = open(os.path.join(args.save, 'val.csv'), 'w')
criterion = medical_zoo.DiceLoss(idx_to_ignore_after=4)
print("START TRAINING...")
for epoch in range(1, args.nEpochs + 1):
train_dice(args, epoch, model, training_generator, optimizer,
criterion, train_f)
dice_loss = test_dice(args, epoch, model, val_generator, optimizer,
criterion, val_f)
is_best = False
if dice_loss < best_prec1:
is_best = True
best_prec1 = dice_loss
utils.save_checkpoint(
{
'epoch': epoch,
'state_dict': model.state_dict(),
'best_prec1': best_prec1
}, is_best, args.save, args.model + "_best")
else:
utils.save_checkpoint(
{
'epoch': epoch,
'state_dict': model.state_dict(),
'best_prec1': best_prec1
}, is_best, args.save, args.model + "_last")
train_f.close()
val_f.close()
def make_rdm_multiple_hierarchy(name,
num_networks,
title="-",
save_files=True,
file_save_name=None,
skips=[]):
if file_save_name == None:
file_save_name = name
# Make one rdm for each network
rdmatrices_left = []
rdmatrices_right = []
for i in range(num_networks + len(skips)):
# Skip number
if skips is not None and i in skips:
continue
model = utils.load_object(name, i)
hidden, _ = accuracy_test_with_goals(model, i)
# Turn a list of tensors into a list of np vectors
for i, tensor in enumerate(hidden):
hidden[i] = tensor.numpy().reshape(-1)
# Now cut that in two and make an RDM for each
cutoff = int(len(hidden[0]) // 2)
left_units = [vector[:cutoff] for vector in hidden]
rdm_left = analysis.rdm_spearman(left_units)
rdmatrices_left.append(rdm_left)
right_units = [vector[cutoff:] for vector in hidden]
rdm_right = analysis.rdm_spearman(right_units)
rdmatrices_right.append(rdm_right)
matrices = []
# Do the same processing for each side (low level/left and high_level/right)
for side in [[rdmatrices_left, "_goals"], [rdmatrices_right, "_actions"]]:
# Now average over all matrices
avg_matrix = None
for matrix in side[0]:
if avg_matrix is None:
avg_matrix = matrix
else:
avg_matrix += matrix
avg_matrix = avg_matrix / num_networks
# delete the unwanted rows and columns:
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 0)
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 1)
nps = 5 # number of elements per sequence
side_name = file_save_name + side[1]
np.savetxt(side_name + "_rdm_mat" + utils.datestr() + ".txt",
avg_matrix,
delimiter="\t",
fmt='%.2e')
labels = []
for i, sequence in enumerate(seqs):
for action in sequence[1:-1]:
labels.append(str(i) + '_' + action)
analysis.plot_rdm(avg_matrix, labels,
title + side_name + " spearman rho matrix")
if save_files:
plt.savefig(side_name + '_rdm' + utils.datestr())
plt.clf()
# nps = 5 # number of elements per sequence
mdsy = analysis.mds(avg_matrix)
for i, style in enumerate(['ro-', 'b|--', 'gx-.']):
analysis.plot_mds_points(mdsy[nps * i:nps * i + nps],
range(nps),
labels=labels[nps * i:nps * i + nps],
style=style)
plt.title(title + side_name)
if save_files:
plt.savefig(side_name + '_mds' + utils.datestr())
plt.clf()
matrices.append(avg_matrix)
return matrices
def make_rdm_multiple_special(name1,
name2,
num_networks,
file_save_name,
title,
skips1=[],
skips2=[]):
mats = []
for name, skips in [(name1, skips1), (name2, skips2)]:
print(name)
# Make one rdm for each network
rdmatrices_left = []
rdmatrices_right = []
for i in range(num_networks + len(skips)):
# Skip number
if skips is not None and i in skips:
continue
model = utils.load_object(name, i)
if name == name1: # Have to do the goal ones first.
hidden = accuracy_test_reg_hierarchy(model, i)
else:
hidden = accuracy_test_reg_hierarchy_nogoals(model, i)
# Turn a list of tensors into a list of np vectors
for i, tensor in enumerate(hidden):
hidden[i] = tensor.numpy().reshape(-1)
# Now cut that in two and make an RDM for each
cutoff = int(len(hidden[0]) // 2)
left_units = [vector[:cutoff] for vector in hidden]
rdm_left = analysis.rdm_spearman(left_units)
rdmatrices_left.append(rdm_left)
right_units = [vector[cutoff:] for vector in hidden]
rdm_right = analysis.rdm_spearman(right_units)
rdmatrices_right.append(rdm_right)
# Do the same processing for each side (low level/left and high_level/right)
for side in [rdmatrices_left, rdmatrices_right]: # goals, then actions
# Now average over all matrices
avg_matrix = None
for matrix in side:
if avg_matrix is None:
avg_matrix = matrix
else:
avg_matrix += matrix
avg_matrix = avg_matrix / num_networks
mats.append(avg_matrix)
# Now average the average matrices
rdmatrices_left = (mats[0] + mats[2]) / 2
rdmatrices_right = (mats[1] + mats[3]) / 2
# Do the same processing for each side (low level/left and high_level/right)
for side in [[rdmatrices_left, "_goals"], [rdmatrices_right, "_actions"]]:
matrix = side[0]
side_name = file_save_name + side[1]
np.savetxt(side_name + "_rdm_mat" + utils.datestr() + ".txt",
matrix,
delimiter="\t",
fmt='%.2e')
labels = []
for i, sequence in enumerate(pnas2018task.seqs):
for action in sequence[1:]:
labels.append(str(i) + '_' + action)
analysis.plot_rdm(matrix, labels,
title + side_name + " spearman rho matrix")
plt.savefig(side_name + '_rdm' + utils.datestr())
plt.clf()
mdsy = analysis.mds(matrix)
for i, style in enumerate(['ro-', 'b|--', 'gx-.', 'k_:']):
analysis.plot_mds_points(mdsy[6 * i:6 * i + 6],
range(6),
labels=labels[6 * i:6 * i + 6],
style=style)
plt.title(title + side_name)
plt.savefig(side_name + '_mds' + utils.datestr())
plt.clf()
def make_rdm_multiple(name,
num_networks,
type="spearman",
with_goals=False,
title="-",
save_files=True,
skips=[]):
# Make one rdm for each network
optimal_list = []
rdmatrices = []
error_per_step = np.zeros((3, 6, 11), dtype=np.float32) # number of steps
hidden_avg = []
hiddens = np.zeros((3, 6), dtype=np.float32)
for i in range(num_networks + len(skips)):
if i in skips:
continue
model = utils.load_object(name, i)
if with_goals:
hidden, optimal = accuracy_test_with_goals(model, i)
else:
hidden, optimal, error_per_step_model = accuracy_test(model, i)
error_per_step += error_per_step_model
optimal_list.append(optimal)
# Turn into a list of simple vectors
for j, tensor in enumerate(hidden):
hidden[j] = tensor.numpy().reshape(-1)
hidden_avg.append(np.average(
hidden[j])) # Get the average activation for that time-step
if type == "spearman":
rdmatrix = analysis.rdm_spearman(hidden)
elif type == "euclidian":
rdmatrix = analysis.rdm_euclidian(hidden)
else:
raise Exception("RDM type " + type + " not implemented")
rdmatrices.append(rdmatrix)
# Now
i = j = 0
for act_avg in hidden_avg:
hiddens[i, j] += act_avg
j += 1
if j > 5:
j = 0
i += 1
if i > 2:
i = 0
j = 0
print(hiddens / num_networks)
print("{0} networks, of which {1} achieve optimal accuracy".format(
num_networks, optimal_list.count(True)))
# Hidden activation per step averages
#for i, hidden_act in enumerate(hidden):
# hidden[i] = np.average(hidden_act)
#hidden_avg = hidden.reshape(18, 11)
#print(enumerate(hidden_avg))
# Error per step averages
error_avg = error_per_step / 100.
error_avg = error_avg.reshape(18, 11)
print(error_avg)
# Now average over all matrices
avg_matrix = None
for matrix in rdmatrices:
if avg_matrix is None:
avg_matrix = matrix
else:
avg_matrix += matrix
avg_matrix = avg_matrix / num_networks
# delete the unwanted rows and columns:
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 0)
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 1)
nps = 5 # number of elements per sequence
if save_files:
np.savetxt(name + "_rdm_mat_" + type + utils.datestr() + ".txt",
avg_matrix,
delimiter="\t",
fmt='%.2e')
np.savetxt(name + "_errors" + utils.datestr() + ".txt",
error_avg,
delimiter="\t",
fmt='%.2e')
labels = []
for i, sequence in enumerate(seqs):
for action in sequence[1:-1]:
labels.append(str(i) + '_' + action)
analysis.plot_rdm(avg_matrix, labels, title + " " + type + " matrix")
if save_files:
plt.savefig(name + '_rdm_' + type)
plt.clf()
mdsy = analysis.mds(avg_matrix)
for i, style in enumerate(['ro-', 'b|--', 'gx-.']):
analysis.plot_mds_points(mdsy[nps * i:nps * i + nps],
range(nps),
labels=labels[nps * i:nps * i + nps],
style=style)
plt.title(title)
if save_files:
plt.savefig(name + '_mds')
plt.clf()
return avg_matrix
def task_dir(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
return '/'.join(
[self.path, 'var', 'cache', ds, uuid[6:8], uuid[21:23], uuid])
def exec_dir(self):
ds = datestr(self.task.created_at)
uuid = self.task.uuid
return '/'.join([self.path, 'var', 'tmp', ds, uuid, self.timestr])
def make_rdm_multiple_predictive(name,
num_networks,
type='sigmoid',
title="-",
save_files=True,
skips=[]):
# Make one rdm for each network
optimal_list = []
rdmatrices = []
for i in range(num_networks + len(skips)):
if i in skips:
continue
model = utils.load_object(name, i)
hidden, optimal = accuracy_test_predictive(model, i, type=type)
optimal_list.append(optimal)
# Turn into a list of simple vectors
for i, tensor in enumerate(hidden):
hidden[i] = tensor.numpy().reshape(-1)
if optimal:
rdmatrix = analysis.rdm_spearman(hidden)
rdmatrices.append(rdmatrix)
print("{0} networks, of which {1} achieve optimal accuracy".format(
num_networks, optimal_list.count(True)))
# Now average over all matrices
avg_matrix = None
for matrix in rdmatrices:
if avg_matrix is None:
avg_matrix = matrix
else:
avg_matrix += matrix
avg_matrix = avg_matrix / len(rdmatrices)
# delete the unwanted rows and columns:
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 0)
avg_matrix = np.delete(avg_matrix, [0, 6, 12], 1)
nps = 5 # number of elements per sequence
if save_files:
np.savetxt(name + "_rdm_mat" + utils.datestr() + ".txt",
avg_matrix,
delimiter="\t",
fmt='%.2e')
labels = []
for i, sequence in enumerate(seqs):
for action in sequence[1:-1]:
labels.append(str(i) + '_' + action)
analysis.plot_rdm(avg_matrix, labels, title + " spearman rho matrix")
if save_files:
plt.savefig(name + '_rdm')
plt.clf()
mdsy = analysis.mds(avg_matrix)
for i, style in enumerate(['ro-', 'b|--', 'gx-.']):
analysis.plot_mds_points(mdsy[nps * i:nps * i + nps],
range(nps),
labels=labels[nps * i:nps * i + nps],
style=style)
plt.title(title)
if save_files:
plt.savefig(name + '_mds')
plt.clf()
return avg_matrix
def make_rdm_multiple_hierarchy_nogoals(name,
num_networks,
title="-",
save_files=True,
file_save_name=None,
cutoff=None):
if file_save_name == None:
file_save_name = name
# Make one rdm for each network
rdmatrices_left = []
rdmatrices_right = []
for i in range(num_networks):
if i == 19:
continue
model = utils.load_object(name, i)
hidden = accuracy_test_reg_hierarchy_nogoals(model, i)
# Turn a list of tensors into a list of np vectors
for i, tensor in enumerate(hidden):
hidden[i] = tensor.numpy().reshape(-1)
# Now cut that in two and make an RDM for each
if cutoff is None:
cutoff = int(len(hidden[0]) // 2)
left_units = [vector[:cutoff] for vector in hidden]
rdm_left = analysis.rdm_spearman(left_units)
rdmatrices_left.append(rdm_left)
right_units = [vector[cutoff:] for vector in hidden]
rdm_right = analysis.rdm_spearman(right_units)
rdmatrices_right.append(rdm_right)
# Do the same processing for each side (low level/left and high_level/right)
for side in [[rdmatrices_left, "_goals"], [rdmatrices_right, "_actions"]]:
# Now average over all matrices
avg_matrix = None
for matrix in side[0]:
if avg_matrix is None:
avg_matrix = matrix
else:
avg_matrix += matrix
avg_matrix = avg_matrix / num_networks
side_name = file_save_name + side[1]
np.savetxt(side_name + "_rdm_mat" + utils.datestr() + ".csv",
avg_matrix,
delimiter=",")
labels = []
for i, sequence in enumerate(pnas2018task.seqs):
for action in sequence[1:]:
labels.append(str(i) + '_' + action)
analysis.plot_rdm(avg_matrix, labels,
title + side_name + " spearman rho matrix")
if save_files:
plt.savefig(side_name + '_rdm' + utils.datestr())
plt.clf()
mdsy = analysis.mds(avg_matrix)
for i, style in enumerate(['ro-', 'b|--', 'gx-.', 'k_:']):
analysis.plot_mds_points(mdsy[6 * i:6 * i + 6],
range(6),
labels=labels[6 * i:6 * i + 6],
style=style)
plt.title(title + side_name)
if save_files:
plt.savefig(side_name + '_mds' + utils.datestr())
plt.clf()
