def process(args):
valset, gpu_index, batch_size = args
os.environ['CUDA_VISIBLE_DEVICES'] = str(gpu_index)
# set iterators for training and validation
val_batch_fetcher = iterator_dr.ValidationBatchFetcher(valset, batch_size)
# load networks
EX_segmentor_dir = "../model/EX_segmentor"
HE_segmentor_dir = "../model/HE_segmentor"
MA_segmentor_dir = "../model/MA_segmentor"
SE_segmentor_dir = "../model/SE_segmentor"
EX_segmentor = utils.load_network(EX_segmentor_dir)
HE_segmentor = utils.load_network(HE_segmentor_dir)
MA_segmentor = utils.load_network(MA_segmentor_dir)
SE_segmentor = utils.load_network(SE_segmentor_dir)
EX_bottleneck_extractor = model.bottleneck_extractor(
EX_segmentor, "activation_14", 0)
HE_bottleneck_extractor = model.bottleneck_extractor(
HE_segmentor, "activation_14", 0)
MA_bottleneck_extractor = model.bottleneck_extractor(
MA_segmentor, "activation_6", 4)
SE_bottleneck_extractor = model.bottleneck_extractor(
SE_segmentor, "activation_10", 2)
for fnames, fundus_rescale, fundus_rescale_mean_subtract, _ in val_batch_fetcher(
):
ex_bottleneck = EX_bottleneck_extractor.predict(fundus_rescale,
batch_size=batch_size,
verbose=0)
he_bottleneck = HE_bottleneck_extractor.predict(
fundus_rescale_mean_subtract, batch_size=batch_size, verbose=0)
ma_bottleneck = MA_bottleneck_extractor.predict(
fundus_rescale_mean_subtract, batch_size=batch_size, verbose=0)
se_bottleneck = SE_bottleneck_extractor.predict(fundus_rescale,
batch_size=batch_size,
verbose=0)
for index in range(ex_bottleneck.shape[0]):
np.save(
os.path.join(out_dirs["EX"], os.path.basename(fnames[index])),
ex_bottleneck[index, ...])
np.save(
os.path.join(out_dirs["HE"], os.path.basename(fnames[index])),
he_bottleneck[index, ...])
np.save(
os.path.join(out_dirs["MA"], os.path.basename(fnames[index])),
ma_bottleneck[index, ...])
np.save(
os.path.join(out_dirs["SE"], os.path.basename(fnames[index])),
se_bottleneck[index, ...])
def __init__(self):
# load images and scale in range (-1, 1)
self.images_loader = utils.load_images('datasets/patterns/')
# dataset = datasets.CIFAR10(root='./cifar10', train=True, download=True, transform=transform)
# dataloader = DataLoader(dataset, batch_size=opt.batch_size, shuffle=True, num_workers=20, drop_last=True)
# load networks
if args.architecture == 'ResNet':
self.encoder = utils.load_network('encoder', waae_resnet.Encoder())
self.decoder = utils.load_network('decoder', waae_resnet.Decoder())
self.discriminator = utils.load_network(
'discriminator', waae_resnet.Discriminator())
# print total and trainable parameters for networks
utils.print_parameters(self.encoder, 'Encoder')
utils.print_parameters(self.decoder, 'Decoder')
utils.print_parameters(self.discriminator, 'Discriminator')
self.reconstruct_loss = torch.nn.MSELoss().cuda(
) if cuda else torch.nn.MSELoss()
# set up optimizers
self.optimizer_R = torch.optim.Adam(itertools.chain(
self.encoder.parameters(), self.decoder.parameters()),
lr=args.lr_R,
betas=(args.b1, args.b2))
self.optimizer_D = torch.optim.Adam(self.discriminator.parameters(),
lr=args.lr_D,
betas=(args.b1, args.b2))
#self.optimizer_D = torch.optim.SGD(self.discriminator.parameters(), lr=args.lr_D, momentum=0.9, dampening=0, weight_decay=1e-4)
self.optimizer_G = torch.optim.Adam(self.encoder.parameters(),
lr=args.lr_G,
betas=(args.b1, args.b2))
# set up LR schedulers
self.scheduler_R = StepLR(self.optimizer_R,
step_size=args.lr_step,
gamma=args.lr_gamma)
self.scheduler_D = StepLR(self.optimizer_D,
step_size=args.lr_step,
gamma=args.lr_gamma)
self.scheduler_G = StepLR(self.optimizer_G,
step_size=args.lr_step,
gamma=args.lr_gamma)
# create batch of latent vectors to visualize the progression of the generator
self.fixed_noise = Variable(
Tensor(np.random.normal(0, args.s_sd, (100, args.latent_dim))))
def main():
log.basicConfig(format = '[ %(levelname)s ] %(message)s',
level = log.INFO, stream = sys.stdout)
args = build_argparser().parse_args()
try:
model_wrapper = openvino_io_model_wrapper()
data_transformer = transformer()
io = io_adapter.get_io_adapter(args, model_wrapper, data_transformer)
iecore = utils.create_ie_core(args.extension, args.cldnn_config, args.device,
args.nthreads, None, args.dump, 'sync', log)
net = utils.create_network(iecore, args.model_xml, args.model_bin, log)
input_shapes = utils.get_input_shape(model_wrapper, net)
for layer in input_shapes:
log.info('Shape for input layer {0}: {1}'.format(layer, input_shapes[layer]))
utils.reshape_input(net, args.batch_size)
log.info('Prepare input data')
io.prepare_input(net, args.input)
log.info('Create executable network')
exec_net = utils.load_network(iecore, net, args.device, args.priority, 1)
log.info('Starting inference ({} iterations) on {}'.
format(args.number_iter, args.device))
result, time = infer_sync(exec_net, args.number_iter, io.get_slice_input)
average_time, latency, fps = process_result(time, args.batch_size, args.mininfer)
if not args.raw_output:
io.process_output(result, log)
result_output(average_time, fps, latency, log)
else:
raw_result_output(average_time, fps, latency)
del net
del exec_net
del iecore
except Exception as ex:
print('ERROR! : {0}'.format(str(ex)))
sys.exit(1)
def occlusion_heatmap(net, image, level=4, square_length=7):
"""
Determines which parts of the image are important for the network classification
Blackens square regions in the image and measures target class probability
See this paper: http://arxiv.org/abs/1311.2901
:param net: a path to a pickeled network or a (net, output) tuple
:param image: an image to test, this function assumes the images has been preprocessed
in the same manner as during net training, otherwise the results are unpredictable
:param level: measure agains this class (currently only class 4 is supported)
:param square_length: size of the square which is blacked out in the image
:return: an array the same size as image with target class probabilities
"""
if isinstance(net, str):
net, output = load_network(net)
else:
net, output = net
img = image.copy()
shape = img.shape
# assume the first layer is InputLayer
net_shape = net[0].get_output_shape()
batch_size = net_shape[0]
assert shape == net_shape[1:]
# allocate network input variable
x_shared = theano.shared(np.zeros(net_shape, dtype=theano.config.floatX),
borrow=True)
# allocate array for the heatmap
heat_array = np.zeros(shape[1:])
pad = square_length // 2
# this will contain images with occluded regions
x_occluded = np.zeros(
(shape[1] * shape[2], net_shape[1], shape[1], shape[2]),
dtype=img.dtype)
# occlude image regions
for i, j in product(*list(map(range, shape[1:]))):
x_padded = np.pad(img, ((0, 0), (pad, pad), (pad, pad)), 'constant')
x_padded[:, i:i + square_length, j:j + square_length] = 0.
x_occluded[i * shape[1] + j, ...] = x_padded[:, pad:-pad, pad:-pad]
predict_proba = theano.function(
[],
output.get_output(x_shared, deterministic=True)[:, level - 1],
)
n_occluded = len(x_occluded)
probas = np.zeros(n_occluded, dtype=theano.config.floatX)
# get the probabilities for occluded images
for b in range(n_occluded / batch_size):
batch_slice = slice(b * batch_size, (b + 1) * batch_size)
x_shared.set_value(x_occluded[batch_slice], borrow=True)
probas[batch_slice] = predict_proba()
#assign probabilities to heat_map
for i, j in product(*list(map(range, shape[1:]))):
heat_array[i, j] = probas[i * shape[1] + j]
return heat_array
def __init__(self):
# load images and scale in range (-1, 1)
self.images_loader = utils.load_images('datasets/patterns/')
# dataset = datasets.CIFAR10(root='./cifar10', train=True, download=True, transform=transform)
# dataloader = DataLoader(dataset, batch_size=opt.batch_size, shuffle=True, num_workers=20, drop_last=True)
# Define the network
self.generator = utils.load_network('generator', dcgan.Generator())
self.discriminator = utils.load_network('discriminator',
dcgan.Discriminator())
# print total and trainable parameters for networks
utils.print_parameters(self.generator, 'Generator')
utils.print_parameters(self.discriminator, 'Discriminator')
self.adversarial_loss = torch.nn.BCELoss().cuda(
) if cuda else torch.nn.BCELoss()
# set up optimisers
self.optimizer_D = torch.optim.RMSprop(self.discriminator.parameters(),
lr=args.lr_d)
self.optimizer_G = torch.optim.RMSprop(self.generator.parameters(),
lr=args.lr_g)
# set up LR schedulers
self.scheduler_D = StepLR(self.optimizer_D,
step_size=args.lr_step,
gamma=args.lr_gamma)
self.scheduler_G = StepLR(self.optimizer_G,
step_size=args.lr_step,
gamma=args.lr_gamma)
# create latent vectors to visualize the progression of the generator
self.fixed_noise = Variable(
Tensor(
np.random.normal(0, args.s_sd,
(args.batch_size, args.latent_dim))))
def gen_user_ked(unfilename, retfilename):
log("Loading user network")
g = load_network(unfilename)
uid2ked = {}
max_nbrksum = 0
log("Computing ked")
for ni in g.Nodes():
# nid = ni.GetId()
k = ni.GetInDeg() # K
nbrks = []
for i in range(k):
nbrnid = ni.GetInNId(i)
nbrni = g.GetNI(nbrnid)
nbrk = nbrni.GetInDeg()
nbrks.append(nbrk)
nbrksum = sum(nbrks)
max_nbrksum = max(max_nbrksum, nbrksum)
for ni in g.Nodes():
nid = ni.GetId()
k = ni.GetInDeg() # K
nbrks = []
for i in range(k):
nbrnid = ni.GetInNId(i)
nbrni = g.GetNI(nbrnid)
nbrk = nbrni.GetInDeg()
if nbrk > 0:
nbrks.append(nbrk)
nbrksum = sum(nbrks)
if k > 1 and nbrksum > 0:
entropy = 0.0
for nbrk in nbrks:
p = nbrk / float(nbrksum)
entropy += -p * math.log(p)
H = entropy / math.log(k) # E
D = math.e ** (nbrksum / float(max_nbrksum)) # D
uid2ked[nid] = k * H * D
else:
uid2ked[nid] = 0.0
with open(retfilename, "w") as retfile:
for uid, ked in uid2ked.iteritems():
retfile.write("%d %.8f\n" % (uid, ked))
def gen_user_hits(unfilename, hubfilename, authfilename):
log('Loading user network')
g = load_network(unfilename)
log('Computing hits')
nid_hub_h = snap.TIntFltH()
nid_auth_h = snap.TIntFltH()
snap.GetHits(g, nid_hub_h, nid_auth_h)
log('Saving results')
with open(hubfilename, 'w') as hubFile:
for nId in nid_hub_h:
hubFile.write('%d %.8f\n' % (nId, nid_hub_h[nId]))
with open(authfilename, 'w') as authFile:
for nId in nid_auth_h:
authFile.write('%d %.8f\n' % (nId, nid_auth_h[nId]))
def gen_user_con_com(unfilename, retfilename):
log('Loading user network')
g = load_network(unfilename)
print g.GetNodes(), g.GetEdges()
# log('Removing single nodes')
# for ni in g.Nodes():
# nodes_to_remove = []
# if ni.GetDeg() == 0:
# nodes_to_remove.append(ni.GetId())
# for nid in nodes_to_remove:
# g.DelNode(nid)
# print g.GetNodes(), g.GetEdges()
log('Computing components')
ccs = snap.TCnComV()
snap.GetSccs(g, ccs)
log('Saving results')
with open(retfilename, 'w') as retfile:
for i, cc in enumerate(ccs):
for nid in cc:
retfile.write('%d %d\n' % (nid, i))
import caffe
import numpy as np
import os
from sklearn import preprocessing
import utils
if __name__ == '__main__':
# ------------------------ Script Parameters ---------------------
batch_size = 10
feature_layers = utils.feature_layers
# feature_layers = ['fc7']
# ------------------------ Script Parameters ---------------------
net, params, blobs = utils.load_network()
image_files = os.listdir(utils.img_dir)
N = len(image_files)
print 'Total Files : ', N
print 'Sample File Name : ', image_files[100]
for layer in feature_layers:
print 'Processing Layer : ' + layer
file = image_files[0]
f0 = caffe.io.load_image(os.path.join(utils.img_dir, file))
prediction = net.predict([f0], oversample=False)
features = net.blobs[layer].data[0]
X = np.zeros((N, features.size), dtype='float32')
ids = []
def __init__(self, gpuID, model_path):
####################################################
# Options
# ------------------
self.gpu_ids = 1
self.which_epoch = '59'
self.batch_size = 1
self.use_dense = False
self.use_PCB = False
self.model_path = model_path
self.class_num = 751
self.score_threshold = 0.9
self.confidence_threshold = 0.6
####################################################
# Set gpu
# ------------------
use_gpu = torch.cuda.is_available()
if not use_gpu:
print('can not user gpu')
exit()
torch.cuda.set_device(self.gpu_ids)
####################################################
# Load model
# ------------------
print('load model...')
if self.use_dense:
model_structure = ft_net_dense(self.class_num)
else:
model_structure = ft_net(self.class_num)
if self.use_PCB:
model_structure = PCB(self.class_num)
model = utils.load_network(model_structure, self.model_path,
self.which_epoch)
# Remove the final fc layer and classifier layer
if not self.use_PCB:
model.model.fc = nn.Sequential()
model.classifier = nn.Sequential()
else:
model = PCB_test(model)
model = model.eval()
#print(model)
if use_gpu:
model = model.cuda()
self.model = model
####################################################
# Set Transform
# ------------------
print('set transform...')
self.data_transforms = transforms.Compose([
transforms.Resize((256, 128), interpolation=3),
transforms.ToTensor(),
transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])
if self.use_PCB:
self.data_transforms = transforms.Compose([
transforms.Resize((384, 192), interpolation=3),
transforms.ToTensor(),
transforms.Normalize([0.485, 0.456, 0.406],
[0.229, 0.224, 0.225])
])
choices=['market1501', 'cuhk03', 'duke'])
parser.add_argument('--batch_size',
default=512,
type=int,
help='batchsize')
parser.add_argument('--share_conv', action='store_true')
arg = parser.parse_args()
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
save_dir_path = os.path.join(arg.save_path, arg.dataset)
logger = utils.Logger(save_dir_path)
logger.info(vars(arg))
# Just to get the correct num_classes of classifier fc
train_dataloader = utils.getDataLoader(arg.dataset, arg.batch_size,
'train')
model = utils.load_network(
PCBModel(num_classes=len(train_dataloader.dataset.classes),
share_conv=arg.share_conv,
return_features=True), save_dir_path, arg.which_epoch)
model = model.to(device)
CMC, mAP, rank_list_fig = test(model, arg.dataset, arg.batch_size)
logger.info('Testing: top1:%.2f top5:%.2f top10:%.2f mAP:%.2f' %
(CMC[0], CMC[4], CMC[9], mAP))
logger.save_img(rank_list_fig)
torch.cuda.empty_cache()
return pd.DataFrame({
"node_id": np.arange(nodes.size),
"mag_journal_id": nodes,
"community_id": cids
})
if __name__ == "__main__":
OUTPUT = sys.argv.pop()
YEARS = [int(y) for y in sys.argv[1:]]
print("years", YEARS)
print("Loading networks")
A, Araw, nodes = utils.load_network(YEARS)
print("Construct graph tool graph object")
G = to_graph_tool(A)
print("Estimating")
states = gt.minimize_blockmodel_dl(
G,
deg_corr=True,
state_args=dict(eweight=G.ep.weight),
verbose=True,
B_max=np.round(A.shape[0] / 3).astype(int),
)
print("Save")
community_table = make_community_table(states, nodes)
def main():
setup_experiment()
data = mnist_load()
X_test = data.X_test
y_test = data.y_test
if FLAGS.sort_labels:
ys_indices = np.argsort(y_test)
X_test = X_test[ys_indices]
y_test = y_test[ys_indices]
img_shape = [None, 1, 28, 28]
test_images = T.tensor4('test_images')
test_labels = T.lvector('test_labels')
# loaded discriminator number of classes and dims
layer_dims = [int(dim) for dim in FLAGS.layer_dims.split("-")]
num_classes = layer_dims[-1]
# create and load discriminator
net = create_network(FLAGS.model, img_shape, layer_dims=layer_dims)
load_network(net, epoch=FLAGS.load_epoch)
model = with_end_points(net)
test_outputs = model(test_images, deterministic=True)
# deepfool images
test_df_images = deepfool(lambda x: model(x, deterministic=True)['logits'],
test_images,
test_labels,
num_classes,
max_iter=FLAGS.deepfool_iter,
clip_dist=FLAGS.deepfool_clip,
over_shoot=FLAGS.deepfool_overshoot)
test_df_images_all = deepfool(
lambda x: model(x, deterministic=True)['logits'],
test_images,
num_classes=num_classes,
max_iter=FLAGS.deepfool_iter,
clip_dist=FLAGS.deepfool_clip,
over_shoot=FLAGS.deepfool_overshoot)
test_df_outputs = model(test_df_images, deterministic=True)
# fast gradient sign images
test_fgsm_images = test_images + fast_gradient_perturbation(
test_images, test_outputs['logits'], test_labels, FLAGS.fgsm_epsilon)
test_at_outputs = model(test_fgsm_images, deterministic=True)
# test metrics
test_acc = categorical_accuracy(test_outputs['logits'], test_labels).mean()
test_err = 1 - test_acc
test_fgsm_acc = categorical_accuracy(test_at_outputs['logits'],
test_labels).mean()
test_fgsm_err = 1 - test_fgsm_acc
test_df_acc = categorical_accuracy(test_df_outputs['logits'],
test_labels).mean()
test_df_err = 1 - test_df_acc
# adversarial noise statistics
reduc_ind = range(1, test_images.ndim)
test_l2_df = T.sqrt(
T.sum((test_df_images - test_images)**2, axis=reduc_ind))
test_l2_df_norm = test_l2_df / T.sqrt(T.sum(test_images**2,
axis=reduc_ind))
test_l2_df_skip = test_l2_df.sum() / T.sum(test_l2_df > 0)
test_l2_df_skip_norm = test_l2_df_norm.sum() / T.sum(test_l2_df_norm > 0)
test_l2_df_all = T.sqrt(
T.sum((test_df_images_all - test_images)**2, axis=reduc_ind))
test_l2_df_all_norm = test_l2_df_all / T.sqrt(
T.sum(test_images**2, axis=reduc_ind))
test_metrics = OrderedDict([('err', test_err), ('err_fgsm', test_fgsm_err),
('err_df', test_df_err),
('l2_df', test_l2_df.mean()),
('l2_df_norm', test_l2_df_norm.mean()),
('l2_df_skip', test_l2_df_skip),
('l2_df_skip_norm', test_l2_df_skip_norm),
('l2_df_all', test_l2_df_all.mean()),
('l2_df_all_norm', test_l2_df_all_norm.mean())
])
logger.info("Compiling theano functions...")
test_fn = theano.function([test_images, test_labels],
outputs=test_metrics.values())
generate_fn = theano.function([test_images, test_labels],
[test_df_images, test_df_images_all],
on_unused_input='ignore')
logger.info("Generate samples...")
samples_per_class = 10
summary_images, summary_labels = select_balanced_subset(
X_test, y_test, num_classes, samples_per_class)
save_path = os.path.join(FLAGS.samples_dir, 'orig.png')
save_images(summary_images, save_path)
df_images, df_images_all = generate_fn(summary_images, summary_labels)
save_path = os.path.join(FLAGS.samples_dir, 'deepfool.png')
save_images(df_images, save_path)
save_path = os.path.join(FLAGS.samples_dir, 'deepfool_all.png')
save_images(df_images_all, save_path)
logger.info("Starting...")
test_iterator = batch_iterator(X_test,
y_test,
FLAGS.batch_size,
shuffle=False)
test_results = np.zeros(len(test_fn.outputs))
start_time = time.time()
for batch_index, (images, labels) in enumerate(test_iterator, 1):
batch_results = test_fn(images, labels)
test_results += batch_results
if batch_index % FLAGS.summary_frequency == 0:
df_images, df_images_all = generate_fn(images, labels)
save_path = os.path.join(FLAGS.samples_dir,
'b%d-df.png' % batch_index)
save_images(df_images, save_path)
save_path = os.path.join(FLAGS.samples_dir,
'b%d-df_all.png' % batch_index)
save_images(df_images_all, save_path)
logger.info(
build_result_str(
"Batch [{}] adversarial statistics:".format(batch_index),
test_metrics.keys(), batch_results))
test_results /= batch_index
logger.info(
build_result_str(
"Test results [{:.2f}s]:".format(time.time() - start_time),
test_metrics.keys(), test_results))
import caffe
image_file = 'ubot5_1.JPG'
layer = 'pool5'
dimension = 256
compression = 'pca'
k = 10
compressor = utils.load_compressor(layer=layer,
dimension=dimension,
compression=compression)
scalar = utils.load_scalar(layer=layer)
net, params, blobs = utils.load_network()
input_image = caffe.io.load_image(os.path.join(utils.instances_dir, image_file))
# predict takes any number of images, and formats them for the Caffe net automatically
prediction = net.predict([input_image], oversample=False)
feat = net.blobs[layer].data[0].ravel()
feat = scalar.transform(feat)
comp_feat = compressor.transform(feat).ravel()
results = sql.query_top_k(k=k,
features=comp_feat,
compression=compression,
layer=layer,
dimension=dimension)
parser = argparse.ArgumentParser()
parser.add_argument("-n",
"--network",
type=str,
default=os.path.join("data", "tidy", "net.pickle"),
help="Path to the pickled network file")
args = parser.parse_args()
netfile = args.network
print("Loading saved network...")
if not os.path.isfile(netfile):
print("No such file: %s" % netfile)
exit()
try:
network, output = load_network(netfile)
except Exception, e:
print("Could not load network: %s" % e)
print("Loading test dataset...")
# load test data chunk
dl = DataLoader(image_size=IMAGE_SIZE)
test_filenames = dl.test_images
n_predictions = len(test_filenames)
print("Compiling theano functions...")
# set up symbolic variables
X = T.tensor4('X')
X_batch = T.tensor4('X_batch')
batch_index = T.iscalar('batch_index')
pred = T.iround(output.get_output(X_batch, deterministic=True))
args = parser.parse_args()
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
# Make saving directory
save_dir_path = os.path.join(args.save_path, args.dataset)
os.makedirs(save_dir_path, exist_ok=True)
logger = utils.Logger(save_dir_path)
logger.info(vars(args))
train_dataloader = getDataLoader(
args.dataset, args.batch_size, args.dataset_path, 'train', shuffle=True, augment=True)
# model = build_model(args.experiment, num_classes=len(train_dataloader.dataset.classes),
# share_conv=args.share_conv)
model = build_model(args.experiment, num_classes=751,
share_conv=args.share_conv)
model = utils.load_network(model,
save_dir_path, args.which_epoch)
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model = model.to(device)
CMC, mAP = test(model, args.dataset, args.dataset_path, args.batch_size)
logger.info('Testing: top1:%.2f top5:%.2f top10:%.2f mAP:%.2f' %
(CMC[0], CMC[4], CMC[9], mAP))
torch.cuda.empty_cache()
"--mean-file",
type=str,
default='',
help="Path to the file storing network configuration")
parser.add_argument("-d",
"--data",
type=str,
default='',
help="Data file")
args = parser.parse_args()
#####################
# Build the model #
#####################
net = load_network(args.network)
print("Loaded network: ")
print_network(net)
# allocate symbolic variables for theano graph computations
X_batch = T.tensor4('x')
data = np.load(args.data)
if args.mean_file:
mean = np.load(args.mean_file)
if args.mean_file:
data = data - mean
x_test = np.rollaxis(data, 3, 1)
'--proba',
dest='proba',
action='store_const',
const=1,
default=0,
help='flag to predict probabilities rather than hard targets')
args = parser.parse_args()
netfile = args.network
print("Loading saved network...")
if not os.path.isfile(netfile):
print(("No such file: %s" % netfile))
exit()
try:
network, output = load_network(netfile)
except Exception as e:
print(("Could not load network: %s" % e))
print("Loading test dataset...")
# load test data chunk
dl = DataLoader(image_size=IMAGE_SIZE,
normalize=True,
batch_size=64,
parallel=False,
train_path="train/trimmed",
test_path=os.path.join("test", "trimmed"))
test_filenames = dl.test_images
n_predictions = len(test_filenames)
print("Compiling theano functions...")
# set up symbolic variables
return np.array(group_embs)
def output_embs():
np.save(args.group_embs, embs)
if __name__ == '__main__':
args = parse_args()
# generatint motifs
cert2idx, idx2size = generate_motif(args.motif_size)
num_motifs = len(cert2idx)
# loading the data
G = load_network(args.network_format, args.network)
groups = load_groups(args.groups)
num_groups = len(groups)
group_ams = []
for group in groups:
group_ams.append(nx.adjacency_matrix(G.subgraph(group)).toarray())
# generating the transition matrices
neighbors_motif_motif, weights_motif_motif, neighbors_motif_group, weights_motif_group, neighbors_group_motif, weights_group_motif = generate_transition_matrices(
)
# generating group corpus
corpus = generate_group_corpus()
# embedding
outputs = model(input_img)
outputs = nn.functional.softmax(outputs)
cams = torch.cat((cams, outputs.data.cpu().float()), 0)
return cams
gallery_path = image_datasets['gallery'].imgs
query_path = image_datasets['query'].imgs
######################################################################
names = opt.names.split(',')
models = nn.ModuleList()
for name in names:
model_tmp, _, epoch = load_network(name, opt)
model_tmp.classifier.classifier = nn.Sequential()
model_tmp = torch.nn.DataParallel(model_tmp)
models.append(model_tmp.cuda().eval())
# Extract feature\
snapshot_feature_mat = './feature/submit_result_%s.mat' % opt.names
print('Feature Output Path: %s' % snapshot_feature_mat)
if not os.path.isfile(snapshot_feature_mat):
with torch.no_grad():
gallery_feature, query_feature = torch.FloatTensor(
), torch.FloatTensor()
for model in models:
q_f = extract_feature(model, dataloaders['query'])
q_f_crop = extract_feature(model, cropped_dataloaders['query'])
q_f = q_f + q_f_crop
2] # "../../data/ThomsonReuters/journal-groups-suspended-by-TR.csv"
CI_DETECTED_DIR = sys.argv[3] # "../../data/cartels"
CLASSIFIED_RESULT = sys.argv[4] # "classified_results.csv"
SAMPLED_CAETELS_FILE = sys.argv[5] # "sampled_"
th = 0.3 # Fraction of citations above which we regard excessive concentration
years = np.arange(2010, 2020) # Years for the detected cartels
# Connect to the database
graph = utils.get_db()
# Load the networks
A_list = {}
node_list = {}
for year in years:
A, _, nodes = utils.load_network(year, NET_DIR)
A_list[year] = A
node_list[year] = nodes
groups_TR = pd.read_csv(TR_DETECTED_FILE, sep="\t")
groups_CI = utils.load_detected_cartels(years, CI_DETECTED_DIR)
# Remove groups that contain at least one suspended journal
suspended_journals = np.unique(groups_TR["mag_journal_id"].values)
contained = [
gid for gid, dg in groups_CI.groupby("gross_group_id")
if ~np.any(np.isin(dg["mag_journal_id"], suspended_journals))
]
unsuspended_groups_CI = utils.slice_groups(groups_CI, contained,
"gross_group_id")
def get_id(img_path):
camera_id = []
labels = []
paths = []
for path, v in img_path:
folder_name = os.path.basename(os.path.dirname(path))
labels.append(int(folder_name))
paths.append(path)
return labels, paths
######################################################################
# Load Collected data Trained model
print('-------test-----------')
model, _, epoch = load_network(opt.name, opt)
model.classifier.classifier = nn.Sequential()
model = model.eval()
if use_gpu:
model = model.cuda()
# Extract feature
since = time.time()
#gallery_name = 'gallery_street'
#query_name = 'query_satellite'
gallery_name = 'gallery_satellite'
#query_name = 'query_street'
#gallery_name = 'gallery_street'
from scipy.sparse import lil_matrix
tf.set_random_seed(0)
np.random.seed(0)
source= 'Blog1'
target = 'Blog2'
emb_filename=str(source)+'_'+str(target)
Kstep=3
####################
# Load source data
####################
A_s, X_s, Y_s= utils.load_network('./input/'+str(source)+'.mat')
num_nodes_S=X_s.shape[0]
####################
# Load target data
####################
A_t, X_t, Y_t = utils.load_network('./input/'+str(target)+'.mat')
num_nodes_T=X_t.shape[0]
features=vstack((X_s, X_t))
features = utils.feature_compression(features, dim=1000)
X_s=features[0:num_nodes_S,:]
X_t=features[-num_nodes_T:,:]
'''compute PPMI'''
def main():
train_dataloader, test_dataloader = get_data_loaders(opt)
capsule_net = load_network(opt)
criterion = nn.MSELoss(reduction='mean').cuda()
optimizer = optim.Adam(capsule_net.parameters(), lr=0.0001)
scheduler = lr_scheduler.StepLR(optimizer, step_size=50, gamma=0.1)
capsule_net.train()
if opt.load_weights != '':
print('Load weights from', opt.load_weights)
capsule_net.module.load_state_dict(torch.load(opt.load_weights))
# =============== TRAIN =========================
global_train_step = 0
global_test_step = 0
best_map = 0
for i, epoch in enumerate(range(opt.nepoch)):
train_loss_sum = 0
true_values_per_joint_per_threshold = np.zeros(
(15, thresholds.shape[0]))
total_examples = 0
capsule_net.train()
print(
f'======>>>>> Online epoch: {epoch}, lr={get_lr(optimizer)} <<<<<======'
)
for data in tqdm(train_dataloader):
global_train_step += 1
points, coords, mean, maxv = data
points, coords = points.cuda(non_blocking=True), coords.cuda(
non_blocking=True)
if points.size(0) < opt.batchSize:
break
optimizer.zero_grad()
estimation, reconstructions = capsule_net(points)
dist1, dist2 = chamfer_dist(reconstructions, points)
reconstruction_loss = (torch.mean(dist1)) + (torch.mean(dist2))
regression_loss = criterion(estimation, coords)
total_loss = reconstruction_loss + regression_loss
total_loss.backward()
optimizer.step()
torch.cuda.synchronize()
writer.add_scalar('train/reconstruction-loss',
reconstruction_loss.detach().cpu().numpy(),
global_step=global_train_step)
writer.add_scalar('train/regression-loss',
regression_loss.detach().cpu().numpy(),
global_step=global_train_step)
points_to_display = np.expand_dims(points.cpu().numpy()[0], axis=0)
reconstructions_to_display = np.expand_dims(
reconstructions.detach().cpu().numpy()[0], axis=0)
points_to_display = ITOPDataset.denormalize(
points_to_display, mean[0].numpy(), maxv[0].numpy())
reconstructions_to_display = ITOPDataset.denormalize(
reconstructions_to_display, mean[0].numpy(), maxv[0].numpy())
writer.add_mesh('train/points',
vertices=points_to_display,
global_step=global_train_step)
writer.add_mesh('train/points-reconstruction',
vertices=reconstructions_to_display,
global_step=global_train_step)
writer.add_scalar('train/lr',
get_lr(optimizer),
global_step=global_train_step)
# mAP calculating
total_examples += len(estimation)
estimation = ITOPDataset.denormalize(
estimation.detach().cpu().numpy(), mean.numpy(), maxv.numpy())
coords = ITOPDataset.denormalize(coords.detach().cpu().numpy(),
mean.numpy(), maxv.numpy())
batch_diff = np.linalg.norm(estimation - coords,
axis=2) # N x JOINT_SIZE
for example in batch_diff:
for i, joint_diff in enumerate(example):
true_values_per_joint_per_threshold[i] += (
joint_diff < thresholds).astype(int)
train_loss_sum += total_loss.item()
scheduler.step()
torch.cuda.synchronize()
map_fig, map_01 = build_map_plot(
thresholds, true_values_per_joint_per_threshold / total_examples)
writer.add_figure('train/map', map_fig, global_step=global_train_step)
# =============== EVAL =========================
test_reconstruction_loss_sum = 0
test_regression_loss_sum = 0
true_values_per_joint_per_threshold = np.zeros(
(15, thresholds.shape[0]))
total_examples = 0
for i, data in enumerate(tqdm(test_dataloader)):
global_test_step += 1
capsule_net.eval()
points, coords, mean, maxv = data
points, coords = points.cuda(), coords.cuda()
estimation, reconstructions = capsule_net(points)
dist1, dist2 = chamfer_dist(points, reconstructions)
test_reconstruction_loss = (torch.mean(dist1)) + (
torch.mean(dist2))
test_regression_loss = criterion(estimation, coords)
test_reconstruction_loss_sum += test_reconstruction_loss.item()
test_regression_loss_sum += test_regression_loss.item()
points_to_display = np.expand_dims(points.cpu().numpy()[0], axis=0)
reconstructions_to_display = np.expand_dims(
reconstructions.detach().cpu().numpy()[0], axis=0)
points_to_display = ITOPDataset.denormalize(
points_to_display, mean[0].numpy(), maxv[0].numpy())
reconstructions_to_display = ITOPDataset.denormalize(
reconstructions_to_display, mean[0].numpy(), maxv[0].numpy())
writer.add_mesh('test/points',
vertices=points_to_display,
global_step=global_test_step)
writer.add_mesh('test/points-reconstruction',
vertices=reconstructions_to_display,
global_step=global_test_step)
# -------- mAP calculating
total_examples += len(estimation)
estimation = ITOPDataset.denormalize(
estimation.detach().cpu().numpy(), mean.numpy(), maxv.numpy())
coords = ITOPDataset.denormalize(coords.detach().cpu().numpy(),
mean.numpy(), maxv.numpy())
batch_diff = np.linalg.norm(estimation - coords,
axis=2) # N x JOINT_SIZE
for example in batch_diff:
for i, joint_diff in enumerate(example):
true_values_per_joint_per_threshold[i] += (
joint_diff < thresholds).astype(int)
avg_reconstruction = test_reconstruction_loss_sum / len(
test_dataloader)
avg_regression = test_regression_loss_sum / len(test_dataloader)
writer.add_scalar('test/reconstruction-loss',
avg_reconstruction,
global_step=global_test_step)
writer.add_scalar('test/regression-loss',
avg_regression,
global_step=global_test_step)
map_fig, map_01 = build_map_plot(
thresholds, true_values_per_joint_per_threshold / total_examples)
writer.add_figure('test/map', map_fig, global_step=global_test_step)
if best_map < map_01:
best_map = map_01
torch.save(
capsule_net.module.state_dict(),
f'{save_dir}/{epoch:03}-{best_map:0.3}-capsule_net-module.pth')
parser.add_argument('--which_epoch',
default='final',
type=str,
help='0,1,2,3,...or final')
parser.add_argument('--dataset', type=str, default='data')
parser.add_argument('--batch_size',
default=32,
type=int,
help='batch_size')
parser.add_argument('--mode_type', default='test', type=str)
arg = parser.parse_args()
# device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
save_path = os.path.join(arg.save_path, arg.dataset)
print('Save_path :: ', save_path)
logger = utils.Logger(save_path)
# model = utils.load_network(Merge_image_text(num_class=len(train_dataloader.dataset.classes),mode=arg.mode_type),
# save_path,arg.which_epoch)
model = utils.load_network(
Merge_image_text(num_class=11003, mode=arg.mode_type), save_path,
arg.which_epoch)
model = model.to(device)
CMC, mAP = test(model, arg.dataset, arg.batch_size)
logger.info('Testing: top1:%.2f top5:%.2f top10:%.2f mAP:%.2f' %
(CMC[0], CMC[4], CMC[9], mAP))
torch.cuda.empty_cache()
parser.add_argument('--lr', default=0.05, type=float, help='learning rate')
parser.add_argument('--droprate', default=0.5, type=float, help='drop rate')
parser.add_argument('--PCB', action='store_true', help='use PCB+ResNet50')
parser.add_argument('--CPB', action='store_true', help='use Center+ResNet50')
parser.add_argument(
'--fp16',
action='store_true',
help='use float16 instead of float32, which will save about 50% memory')
parser.add_argument('--balance', action='store_true', help='balance sample')
parser.add_argument('--angle', action='store_true', help='use angle loss')
parser.add_argument('--arc', action='store_true', help='use arc loss')
parser.add_argument('--resume', action='store_true', help='use arc loss')
opt = parser.parse_args()
if opt.resume:
model, opt, start_epoch = load_network(opt.name, opt)
else:
start_epoch = 0
print(start_epoch)
fp16 = opt.fp16
data_dir = opt.data_dir
name = opt.name
if not opt.resume:
str_ids = opt.gpu_ids.split(',')
gpu_ids = []
for str_id in str_ids:
gid = int(str_id)
if gid >= 0:
EX_segmentor_dir = "../model/EX_segmentor"
HE_segmentor_dir = "../model/HE_segmentor"
MA_segmentor_dir = "../model/MA_segmentor"
SE_segmentor_dir = "../model/SE_segmentor"
for task in ["EX", "HE", "MA", "SE"]:
if not os.path.isdir(os.path.join(img_out_dir, task)):
os.makedirs(os.path.join(img_out_dir, task))
# set iterators for training and validation
training_set, validation_set = utils.split_dr(fundus_dirs, grade_path,
val_ratio)
val_batch_fetcher = iterator_dr_640.ValidationBatchFetcher(
validation_set, batch_size)
EX_segmentor = utils.load_network(EX_segmentor_dir)
HE_segmentor = utils.load_network(HE_segmentor_dir)
MA_segmentor = utils.load_network(MA_segmentor_dir)
SE_segmentor = utils.load_network(SE_segmentor_dir)
# normalization_method
# EX, SE: rescale
# HE, MA: rescale_mean_subtract
# network input order: ex, he, ma, se
for fnames, fundus_rescale, fundus_rescale_mean_subtract, grades in val_batch_fetcher(
):
# debugging purpose
ex_arr = EX_segmentor.predict(fundus_rescale,
batch_size=batch_size,
verbose=0)
he_arr = HE_segmentor.predict(fundus_rescale_mean_subtract,
cont_encoder = model.cont_encoder(opt.z_dim*opt.factor, opt.channels*opt.n_past) #g_dim = 64 or 128
pose_encoder = model.pose_encoder(opt.g_dim, opt.channels)
decoder = model.decoder(opt.g_dim, opt.channels)
# init
frame_predictor = utils.init_net(frame_predictor, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
posterior_pose = utils.init_net(posterior_pose, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
prior = utils.init_net(prior, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
cont_encoder = utils.init_net(cont_encoder, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
pose_encoder = utils.init_net(pose_encoder, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
decoder = utils.init_net(decoder, init_type='normal', init_gain=0.02, gpu_ids=opt.gpu_ids)
# load
utils.load_network(frame_predictor, 'frame_predictor', 'last', opt.model_path,device)
utils.load_network(posterior_pose, 'posterior_pose', 'last', opt.model_path,device)
utils.load_network(prior, 'prior', 'last', opt.model_path,device)
utils.load_network(cont_encoder, 'cont_encoder', 'last', opt.model_path,device)
utils.load_network(pose_encoder, 'pose_encoder', 'last', opt.model_path,device)
utils.load_network(decoder, 'decoder', 'last', opt.model_path,device)
frame_predictor.eval()
prior.eval()
posterior_pose.eval()
cont_encoder.eval()
pose_encoder.eval()
decoder.eval()
"--network",
type=str,
help="Path to the pickled network file")
parser.add_argument("-m",
"--mean-file",
type=str,
default='',
help="Path to the file storing network configuration")
parser.add_argument("-d", "--data", type=str, default='', help="Data file")
args = parser.parse_args()
#####################
# Build the model #
#####################
net = load_network(args.network)
print("Loaded network: ")
print_network(net)
# allocate symbolic variables for theano graph computations
X_batch = T.tensor4('x')
data = np.load(args.data)
if args.mean_file:
mean = np.load(args.mean_file)
if args.mean_file:
data = data - mean
x_test = np.rollaxis(data, 3, 1)
from parameter import get_parameter
from utils import load_network, save_network
from train import train_network
from evaluate import test_network
from hardprune import hard_prune_network
from softprune import soft_prune_network
import os
os.environ["CUDA_VISIBLE_DEVICES"] = "2"
if __name__ == '__main__':
args = get_parameter()
network = load_network(args)
print(network)
if args.train_flag:
print('args.train_flag:', args.train_flag)
network = train_network(network, args)
elif args.hard_prune_flag:
print('hard_prune_flag:', args.hard_prune_flag)
network = hard_prune_network(network, args)
elif args.soft_prune_flag:
network = soft_prune_network(network, args)
print(network)
test_network(network, args)
# network = train_network(network, args)
save_network(network, args)
if not os.path.isdir(img_out_dir):
os.makedirs(img_out_dir)
if not os.path.isdir(train_img_check_dir):
os.makedirs(train_img_check_dir)
if not os.path.isdir(val_img_check_dir):
os.makedirs(val_img_check_dir)
# set iterator
training_set, validation_set = utils.split(fundus_dir, vessel_dir, grade_path,
FLAGS.grade_type, 1)
val_batch_fetcher = iterator_dme.ValidationBatchFetcher(
validation_set, batch_size, FLAGS.grade_type)
# create networks
K.set_learning_phase(False)
EX_segmentor = utils.load_network(EX_segmentor_dir)
fovea_localizer = utils.load_network(fovea_localizer_dir)
od_segmentor = utils.load_network(od_segmentor)
# start inference
check_train_batch, check_validation_batch = True, True
list_grades, list_od_found, list_sum_intensity_inside, list_sum_intensity_outside, list_fnames = [], [], [], [], []
for fnames, imgs_mean_subt, imgs_z, vessels, grades_onehot in val_batch_fetcher(
):
if check_validation_batch:
utils.check_input(imgs_mean_subt, imgs_z, vessels, val_img_check_dir)
check_validation_batch = False
segmented = EX_segmentor.predict(imgs_mean_subt,
batch_size=batch_size,
verbose=0)
fovea_loc, fovea_loc_vessel = fovea_localizer.predict(
import matplotlib
import matplotlib.pyplot as plt
def convert_row(row):
a, b, c, d = utm.from_latlon(row['lat'], row['lon'], force_zone_number = 1, force_zone_letter = 'S')
row['lat'] = a
row['lon'] = b
return row
def to_utm(data ):
return data.apply(convert_row, axis=1)
nodes, links = load_network('/home/pestka/Documents/studia/pszt/proj3/sndlib-networks-native/polska.txt')
# nodes = to_utm(nodes)
name_map = {r['name']:(r['lat'], r['lon']) for i, r in nodes.iterrows()}
MAX_COST = links.cost.map(float).max() / 3.
for i, row in links.iterrows():
p1 = name_map[row['source']]
p2 = name_map[row['target']]
plt.plot([p1[1], p2[1]], [p1[0], p2[0]], c='gray', linewidth = float(row['cost']) / MAX_COST)
plt.scatter(x=nodes.lon, y=nodes.lat)
plt.show()
action='store_true',
help='use resume trainning')
parser.add_argument('--share',
action='store_true',
help='share weight between different view')
parser.add_argument('--extra_Google',
action='store_true',
help='using extra noise Google')
parser.add_argument(
'--fp16',
action='store_true',
help='use float16 instead of float32, which will save about 50% memory')
opt = parser.parse_args()
if opt.resume:
model, opt, start_epoch = load_network(opt.name, opt)
else:
start_epoch = 0
fp16 = opt.fp16
data_dir = opt.data_dir
name = opt.name
str_ids = opt.gpu_ids.split(',')
gpu_ids = []
for str_id in str_ids:
gid = int(str_id)
if gid >= 0:
gpu_ids.append(gid)
# set gpu ids
if len(gpu_ids) > 0:
#
# Parameters
#
if __name__ == "__main__":
YEAR = int(sys.argv[1])
NETWORK_DIR = sys.argv[2]
THETA = float(sys.argv[3])
ALPHA = float(sys.argv[4])
COMMUNITY_FILE = sys.argv[5]
OUTPUT = sys.argv[6]
# Load the network data
A_eff, A_gen, nodes = utils.load_network(YEAR, NETWORK_DIR)
# Load the communty membership
community_table = pd.read_csv(COMMUNITY_FILE, sep="\t")
community_ids = (
community_table.set_index("mag_journal_ids").loc[nodes, "community_id"].values
)
# Define the filter
is_excessive_func = filters.get_dcsbm_threshold_filter(
A_eff, A_gen, community_ids, ref_frac_weight=0.5, alpha=ALPHA
)
# Detect cartel
cartel_table = cidre.detect(A_eff, THETA, is_excessive_func, min_group_edge_num=50)
