def train():
video_dir = os.path.join(parentUrl, 'data', 'train', 'lab')
box_to_vect_dataset = BoxToVectDataSet(
train_set_file='data/train.npy',
val_set_file='data/val.npy',
video_files=[
os.path.join(video_dir, '4p-c0.avi'),
os.path.join(video_dir, '4p-c1.avi'),
os.path.join(video_dir, '4p-c2.avi'),
os.path.join(video_dir, '4p-c3.avi'),
],
test_set_file=None,
image_width=Config['image_width'],
image_height=Config['image_height'])
box_to_vect = Resnet(
image_height=Config['image_height'],
image_width=Config['image_width'],
vector_dim=128,
alpha=Config['alpha'],
feature_map_layer='block_layer3',
resnet_size=18,
data_format='channels_first',
mode='train',
init_learning_rate=0.001,
optimizer_name='adam',
batch_size=Config['batch_size'],
max_step=Config['max_step'],
model_path='model/',
logdir='log/',
)
with tf.Session() as sess:
box_to_vect.train(box_to_vect_dataset, sess)
def classify_train(name, learning_rate, init_weight=None):
print('start classify_train')
net = Resnet()
#net = SimpleVgg()
model = net.get_model(learning_rate)
if not init_weight == None:
model.load_weights(init_weight)
model.summary()
generator = DataGenerator(name=name)
run = '{}-{}-{}'.format(name,
time.localtime().tm_hour,
time.localtime().tm_min)
log_dir = CLASSIFY_LOG_DIR.format(run)
check_point = log_dir + '/' + name + '_checkpoint-{epoch:02d}-{val_loss:.4f}.hdf5'
print("classify train round {}".format(run))
tensorboard = TensorBoard(log_dir=log_dir, write_graph=False)
checkpoint = ModelCheckpoint(filepath=check_point,
monitor='val_loss',
verbose=1,
save_best_only=True)
early_stopping = EarlyStopping(monitor='val_loss',
patience=TRAIN_EARLY_STOPPING,
verbose=1)
model.fit_generator(
generator.flow_classfication(mode='train'),
steps_per_epoch=TRAIN_STEPS_PER_EPOCH,
validation_data=generator.flow_classfication(mode='val'),
validation_steps=TRAIN_VALID_STEPS,
epochs=TRAIN_EPOCHS,
verbose=1,
callbacks=[tensorboard, checkpoint, early_stopping])
def build(self, hp):
maxnorm = hp.Choice('maxnorm', values=self.hyperparam['maxnorm'])
resnet_model = Resnet(input_shape=(self.seqlen, self.channels), norm_max=maxnorm)
if self.pretrained_weights is not None:
resnet_model.set_weights(self.pretrained_weights)
inp = Input(shape=(self.seqlen, self.channels))
enc_inp = resnet_model(inp)
dense_units = hp.Int('preclassification', min_value = self.hyperparam['dense_units']['min'],\
max_value = self.hyperparam['dense_units']['max'], step = self.hyperparam['dense_units']['step'])
dense_out = Dense(units = dense_units, activation='relu',
kernel_constraint=MaxNorm(maxnorm,axis=[0,1]),
bias_constraint=MaxNorm(maxnorm,axis=0),
kernel_initializer=glorot_uniform(seed=0))(enc_inp)
dense_out = Dropout(rate=hp.Choice('dropout', values = self.hyperparam['dropout']))(dense_out)
output = Dense(self.num_classes, activation='softmax',
kernel_constraint=MaxNorm(maxnorm,axis=[0,1]),
bias_constraint=MaxNorm(maxnorm,axis=0),
kernel_initializer=glorot_uniform(seed=0))(dense_out)
model = Model(inputs=inp, outputs=output)
model.compile(optimizer=Adam(lr=hp.Choice('lr', values = self.hyperparam['lr'])),
loss=focal_loss(), metrics=['accuracy', macro_f1])
return model
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], 'i:o:r:c:',
['images=', 'labels=', 'resize=', 'crop='])
except getopt.GetoptError as err:
print(err)
sys.exit()
ipath, lpath = '', ''
resize, crop = [0, 0], [0, 0]
for o, a in opts:
if o in ('-i', '--images') and type(a) == str:
ipath = a
elif o in ('-l', '--labels') and type(a) == str:
lpath = a
elif o in ('-r', '--resize') and type(a) == int:
resize = [a, a]
elif o in ('-c', '-crop') and type(a) == int:
crop = [a, a]
else:
assert False, 'unhandled option'
res = Resnet()
res.input(ipath=ipath, lpath=lpath, resize=resize, crop=crop)
res.compile_model()
res.callback()
res.train()
def predict():
model = Resnet()
# original saved file with DataParallel
state_dict = torch.load('sgdr_rgb.pkl')
# create new OrderedDict that does not contain `module.`
new_state_dict = OrderedDict()
for k, v in state_dict.items():
name = k[7:] # remove `module.`
new_state_dict[name] = v
# load params
model.load_state_dict(new_state_dict)
#model.load_state_dict(torch.load('best.pkl'))
th = choose_th(model)
handle(model, th)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], 'i:o:r:c:m:', ['inpath=','outpath=','resize=','crop=','modelpath='])
except getopt.GetoptError as err:
print(err)
sys.exit()
ipath,opath = '',''
resize,crop = [0,0],[0,0]
loadpath = None
for o, a in opts:
if o in ('-i', '--inpath') and type(a)==str:
ipath = a
elif o in ('-o', '--outpath') and type(a)==str:
opath = a
elif o in ('-r', '--resize') and type(a)==int:
resize = [a,a]
elif o in ('-c', '--crop') and type(a)==int:
crop = [a,a]
elif o in ('-m', '--modelpath') and type(a)==str:
modelpath = a
else:
assert False, 'unhandled option'
res = Resnet()
if loadpath != None:
res.load_model(modelpath)
res.input(ipath=ipath,lpath=None,resize=resize,crop=crop)
res.test(opath)
def experiment(num_blocks, conv, learning_rate, rate, epochs, name):
global net
print 'Resnet ' + `num_blocks` + '-blocks, conv=' + conv.__name__ + ', learning rate=' + `learning_rate` + ', rate=' + `rate` + '\n'
tf.reset_default_graph()
net = None
net = Resnet(n=num_blocks, conv=conv, rate=rate)
run_session(net, name, learning_rate, epochs)
print ''
def __init__(self):
super(TripletNet, self).__init__()
self.backbone = Resnet(mode='resnet34')
self.pool = torch.nn.AdaptiveAvgPool2d(output_size=(1, 1))
self.fc = torch.nn.Linear(in_features=512,
out_features=128,
bias=False)
self.dropout = torch.nn.Dropout(p=0.2)
def predict_test_only_classification():
net = Resnet()
name = 'Resnet'
model = net.get_model()
model.load_weights(CLASS_MODEL_PATH)
columns = [
'seriesuid', 'coordX', 'coordY', 'coordZ', 'class', 'probability'
]
df = pd.DataFrame(columns=columns)
#Use two round to detect. same step,different start point
print('Round 1')
df = predict_box(np.array([16, 16, 16]), model, columns, df)
print('Round 2')
df = predict_box(np.array([0, 0, 0]), model, columns, df)
df.to_csv('./output/result_only_class.csv', index=False)
def main():
args = parse_args()
if args is None:
exit()
with tf.Session(config=tf.ConfigProto(allow_soft_placement=True)) as sess:
cnn = Resnet(sess,args)
cnn.build_model()
show_all_variables()
if args.phase=='train':
cnn.train()
print('Train finished! \n')
cnn.test()
print('Test finished!')
if args.phase=='test':
cnn.test()
print('Test finished!!')
def main(argv):
infile = argv[0]
outfile = argv[1]
seqlen = 1500
channels = 6
maxnorm = 20.0
# Create model
resnet_model = Resnet(input_shape=(seqlen, channels), norm_max=maxnorm)
samp1 = Input(shape=(seqlen, channels))
enc_samp1 = resnet_model(samp1)
samp2 = Input(shape=(seqlen, channels))
enc_samp2 = resnet_model(samp2)
diff_layer = Lambda(lambda tensors: K.abs(tensors[0] - tensors[1]))
diff_enc = diff_layer([enc_samp1, enc_samp2])
dense_out = Dense(50,
activation='relu',
kernel_constraint=MaxNorm(maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0))(diff_enc)
dense_out = Dropout(rate=0.2)(dense_out)
output = Dense(1,
activation='sigmoid',
kernel_constraint=MaxNorm(maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0))(dense_out)
model = Model(inputs=[samp1, samp2], outputs=output)
model.load_weights(infile)
for layer in model.layers:
if layer.name == "model":
resnet_model.set_weights(layer.get_weights())
resnet_model.save_weights(outfile)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--data", help="cifar data path", default="../data/cifar-10-batches-py")
parser.add_argument("--epochs", type=int, help="number of learning epoch, default is 10", default=10)
parser.add_argument("--saving", help="wheter saving or not(each verbose iteration)", action="store_true")
parser.add_argument("--batch_size", type=int, help="batch size(default is 32)", default=32)
parser.add_argument("--verbose", type=int, help="verbosity cycle(default is 1 epoch)", default=1)
parser.add_argument("--no_tqdm", help="whether to use tqdm process bar", action="store_true")
parser.add_argument("--lr", type=float, help="learning rate, default is 0.001", default=1e-3)
args = parser.parse_args()
dirname = args.data
X_train, y_train = prerprocess_train(dirname)
X_test, y_test = prerprocess_test(dirname)
device = 'gpu:0' if tfe.num_gpus() > 0 else 'cpu:0'
resnet_model = Resnet(learning_rate=args.lr, device_name=device)
resnet_model(tf.convert_to_tensor(X_train[:1]), True)
resnet_model.summary()
# resnet_model.load() # you can load the latest model you saved
if args.no_tqdm:
tqdm_option = None
else:
tqdm_option = "normal"
resnet_model.fit(X_train, y_train, X_test, y_test, epochs=args.epochs, verbose=args.verbose,
batch_size=args.batch_size, saving=args.saving, tqdm_option=tqdm_option)
def create_resnet_model(seqlen, num_channels, maxnorm, modeldir, dense_units,
num_classes):
resnet_model = Resnet(input_shape=(seqlen, num_channels), norm_max=maxnorm)
# Load weights from pretrained model
resnet_model.load_weights(os.path.join(modeldir, 'pretrained_resnet.h5'))
samp = Input(shape=(seqlen, num_channels))
enc_samp = resnet_model(samp)
dense_out = Dense(dense_units,
activation='relu',
kernel_constraint=MaxNorm(maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0),
name='FC1')(enc_samp)
dense_out = Dropout(rate=0.2)(dense_out)
output = Dense(num_classes,
activation='softmax',
kernel_constraint=MaxNorm(maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0),
name='output')(dense_out)
model = Model(inputs=samp, outputs=output)
return model
def __init__(self, arch_cnn='densenet'):
super(discriminator, self).__init__()
if arch_cnn.lower() == 'densenet':
self.cnn_backbone = Densenet()
print('|------Initiating Discriminator: Densenet ------|')
if arch_cnn.lower() == 'resnet':
self.cnn_backbone = Resnet()
print('|------Initiating Discriminator: Resnet ------|')
self.l2_norm = l2_normalize_embedding()
self.classifier = nn.Sequential(nn.Linear(2000, 4000, bias=True),
nn.ReLU(), nn.Linear(4000,
2,
bias=True))
self.classifier_2 = nn.Sequential(nn.Linear(1000, 2000, bias=True),
nn.ReLU(),
nn.Linear(2000, 27, bias=True))
def update_learning_rate(current_lr, optimizer):
new_lr = current_lr/10
for g in optimizer.param_groups:
g['lr'] = new_lr
return new_lr
if __name__ == '__main__':
use_cuda = len(sys.argv) > 1 and sys.argv[1] == 'cuda'
num_epochs = 80
# get cifar 10 data
trainloader, testloader = get_dataset()
benchmark, debug = False, True
resnet = Resnet(n=2,dbg=debug)
resnet.train()
if use_cuda:
resnet = resnet.cuda()
for block in resnet.residual_blocks:
block.cuda()
current_lr = 1e-4
# optimizer = optim.SGD(resnet.parameters(), lr=current_lr, weight_decay=0.0001, momentum=0.9)
optimizer = optim.Adam(resnet.parameters(), lr=1e-4, weight_decay=0.0001)
train_accs, test_accs = [], []
gradient_norms = []
def train_model():
current_lr=1e-4
stopping_threshold, current_count = 3, 0
n_iters = 0
for e in range(num_epochs):
def main(argv):
indir = args.indir
outdir = args.outdir
if not os.path.exists(outdir):
os.makedirs(outdir)
dirstr = 'lr{:.4f}-maxnorm{:.2f}-batchsize{:d}'.format(
args.lr, args.maxnorm, args.batchsize)
resultdir = os.path.join(outdir, dirstr)
if not os.path.exists(resultdir):
os.makedirs(resultdir)
# Hyperparameters
lr = args.lr # learning rate
num_epochs = args.num_epochs
batch_size = args.batchsize
# Read train data
ftrain = h5py.File(os.path.join(args.indir, 'train_dataset.h5'), 'r')
train_samples1 = ftrain['samp1']
train_samples2 = ftrain['samp2']
train_labels = np.array(ftrain['label'], dtype=np.int32)
[num_train, seqlen, channels] = train_samples1.shape
# Read validation data
fval = h5py.File(os.path.join(args.indir, 'val_dataset.h5'), 'r')
val_samples1 = fval['samp1']
val_samples2 = fval['samp2']
val_labels = np.array(fval['label'], dtype=np.int32)
[num_val, seqlen, channels] = val_samples1.shape
# Read test data
ftest = h5py.File(os.path.join(args.indir, 'test_dataset.h5'), 'r')
test_samples1 = ftest['samp1']
test_samples2 = ftest['samp2']
test_labels = np.array(ftest['label'], dtype=np.int32)
[num_test, seqlen, channels] = test_samples1.shape
# Data generators for train/val/test
train_gen = DataGenerator(train_samples1, train_samples2, train_labels,\
batch_size=batch_size, seqlen=seqlen, channels=channels,\
shuffle=True, balance=True, augment=False, aug_factor=0.25)
val_gen = DataGenerator(val_samples1, val_samples2, val_labels,\
batch_size=batch_size, seqlen=seqlen, channels=channels)
test_gen = DataGenerator(test_samples1, test_samples2, test_labels,\
batch_size=batch_size, seqlen=seqlen, channels=channels)
# Create model
resnet_model = Resnet(input_shape=(seqlen, channels),
norm_max=args.maxnorm)
samp1 = Input(shape=(seqlen, channels))
enc_samp1 = resnet_model(samp1)
samp2 = Input(shape=(seqlen, channels))
enc_samp2 = resnet_model(samp2)
diff_layer = Lambda(lambda tensors: K.abs(tensors[0] - tensors[1]))
diff_enc = diff_layer([enc_samp1, enc_samp2])
dense_out = Dense(50,
activation='relu',
kernel_constraint=MaxNorm(args.maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(args.maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0))(diff_enc)
dense_out = Dropout(rate=0.2)(dense_out)
output = Dense(1,
activation='sigmoid',
kernel_constraint=MaxNorm(args.maxnorm, axis=[0, 1]),
bias_constraint=MaxNorm(args.maxnorm, axis=0),
kernel_initializer=glorot_uniform(seed=0))(dense_out)
model = Model(inputs=[samp1, samp2], outputs=output)
model.compile(optimizer=Adam(lr=lr),
loss=BinaryCrossentropy(),
metrics=['accuracy'])
# Train model
# Use early stopping and model checkpoints to handle overfitting and save best model
model_checkpt = ModelCheckpoint(os.path.join(resultdir,'{epoch:02d}-{val_accuracy:.4f}.h5'),\
monitor='val_accuracy')#,\
#mode='max', save_best_only=True)
batch_renorm_cb = BatchRenormScheduler(
len(train_gen)) # Implement batchrenorm after 1st epoch
history = model.fit(train_gen,
epochs=num_epochs,
validation_data=val_gen,
verbose=1,
shuffle=False,
callbacks=[batch_renorm_cb, model_checkpt],
workers=2,
max_queue_size=20,
use_multiprocessing=False)
# Plot training history
plot_results(history.history['loss'], history.history['val_loss'],\
os.path.join(resultdir,'loss.jpg'), metric='Loss')
plot_results(history.history['accuracy'], history.history['val_accuracy'],\
os.path.join(resultdir,'accuracy.jpg'), metric='Accuracy')
# Predict probability on validation data using best model
best_model_file, epoch, val_accuracy = get_best_model(resultdir)
print(
'Predicting with model saved at Epoch={:d} with val_accuracy={:0.4f}'.
format(epoch, val_accuracy))
model.load_weights(os.path.join(resultdir, best_model_file))
probs = model.predict(test_gen)
y_pred = probs.argmax(axis=1)
y_true = test_labels
test_acc = accuracy_score(y_true, y_pred)
print('Test accuracy = {:0.2f}'.format(test_acc * 100.0))
categorical_ce_beta_regularized(ds.num_classes, eta=ETA)
}
LOSS = loss_options[args.loss]
METRICS = ['accuracy']
BATCH_SIZE = args.batch
EPOCHS = 100
for fold in range(args.fold, ds.n_folds):
ds.set_fold(fold)
# Remove old graph and create a new one keeping the same seeds
reset_keras(1)
# Create resnet model
l_in = keras.layers.Input(ds.sample_shape)
output = Resnet(l_in)
output = keras.layers.Flatten()(output)
# Create model output
if args.output == 'softmax':
output = keras.layers.Dense(
ds.num_classes,
kernel_initializer=keras.initializers.he_normal(),
bias_initializer=keras.initializers.Constant(0))(output)
output = keras.layers.Softmax()(output)
elif args.output == 'stick':
output = stick_breaking_layers(output, ds.num_classes)
model = keras.models.Model(l_in, output, name='Resnet')
# Compile the model
height=224,
width=224)
tr_data = ImageNetGenerator(hparams)
tr_iterator = tr_data.get_iterator()
hparams.txt_file = "dev.txt"
hparams.is_training = False
hparams.shuffle = False
dev_data = ImageNetGenerator(hparams)
dev_iterator = dev_data.get_iterator()
X = tf.placeholder(tf.float32, [None, 224, 224, 3])
y = tf.placeholder(tf.float32, [None, hparams.num_classes])
is_training = tf.placeholder(tf.bool)
learning_rate = tf.Variable(0.0, trainable=False)
model = Resnet(is_training)
y_ = model.create_model(X)
loss, loss_summary = model.cross_entropy(y_, y)
train_op, gradient_summary = model.optimizer(loss, learning_rate)
accuracy, accuracy_summary = model.accuracy(y_, y)
train_summary = tf.summary.merge(loss_summary + gradient_summary +
accuracy_summary)
saver = tf.train.Saver()
with tf.Session() as sess:
ckpt = tf.train.get_checkpoint_state('./ckpt')
if ckpt and tf.train.checkpoint_exists(ckpt.model_checkpoint_path):
print("Reading model parameters from %s" %
ckpt.model_checkpoint_path)
saver.restore(sess, ckpt.model_checkpoint_path)
else:
from examples.mt_model import Mt_model
from resnet import Resnet
network = Resnet()
model = Mt_model(Network=network,
ckpt_path='a',
tsboard_path='n',
x_shape=[None, 86, 1])
return opt_img
if __name__ == '__main__':
transform = transforms.Compose([transforms.RandomResizedCrop(224),transforms.ToTensor() ,transforms.Normalize((0.5 , 0.5 , 0.5) , (0.5 , 0.5 , 0.5))])
# trainset = torchvision.datasets.CIFAR10(root = './data' , train = True , download = True , transform = transform)
# trainloader = torch.utils.data.DataLoader(trainset , batch_size = 256 , shuffle = True , num_workers =2)
testset = torchvision.datasets.CIFAR10(root = './data' , train = False , download = True , transform = transform)
testloader = torch.utils.data.DataLoader(testset , batch_size = 9 , shuffle = False , num_workers = 2)
# classes = ('plane' , 'car' , 'bird' , 'cat' , 'deer' , 'dog' , 'frog' , 'horse' , 'ship' , 'truck')
os.environ['CUDA_VISIBLE_DEVICES'] = "3"
#
#
resnet = Resnet()
device_ids=[0]
resnet = resnet.cuda(device_ids[0])
net=torch.nn.DataParallel(resnet,device_ids=device_ids)
#
# read model
print('===> Try load checkpoint')
if os.path.isdir('checkpoint'):
try:
checkpoint = torch.load('./checkpoint/resnet_final.t7')
net.load_state_dict(checkpoint['state'])
start_epoch = checkpoint['epoch']
print('===> Load last checkpoint data')
except FileNotFoundError:
start_epoch = 0
print('Can\'t found resnet_final.t7')
def __init__(self,
mode,
rpn_anchor_ratios,
rpn_anchor_scales,
mask_shape,
pool_size,
image_shape,
mini_mask_shape,
backbone_strides,
mean_pixel,
roi_size=7,
backbone='resnet50',
stage5=True,
norm='batch',
use_bias=True,
rpn_anchor_stride=1,
image_per_gpu=1,
gpu_count=1,
detection_max_instances=100,
train_rois_per_image=200,
num_classes=1,
use_mini_mask=True,
use_pretrained_model=True,
top_down_pyramid_size=256,
post_nms_rois_training=2000,
post_nms_rois_inference=1000,
pre_nms_limit=6000,
rpn_nms_threshold=0.7,
use_rpn_rois=True,
model_dir=None,
optimizer_method='Adam',
learning_rate=0.001,
momentum=0.9,
weight_decay=0.0001,
image_min_dim=800,
image_max_dim=1024,
image_min_scale=0.0,
image_resize_mode='square',
max_gt_instances=100,
rpn_train_anchors_per_image=256):
assert mode in ['training', 'inference']
assert optimizer_method in ['Adam', 'SGD']
tf.reset_default_graph()
self.graph = tf.Graph()
self.mode = mode
self.rpn_anchor_ratios = rpn_anchor_ratios
self.rpn_anchor_scales = rpn_anchor_scales
self.mask_shape = mask_shape
self.pool_size = pool_size
self.image_shape = np.array(image_shape)
self.mini_mask_shape = mini_mask_shape
self.backbone_strides = backbone_strides
self.mean_pixel = mean_pixel
self.roi_size = roi_size
self.backbone = backbone
self.stage5 = stage5
self.norm = norm
self.use_bias = use_bias
self.rpn_anchor_stride = rpn_anchor_stride
self.image_per_gpu = image_per_gpu
self.gpu_count = gpu_count
self.detection_max_instances = detection_max_instances
self.train_rois_per_image = train_rois_per_image
self.num_classes = num_classes
self.use_mini_mask = use_mini_mask
self.use_pretrained_model = use_pretrained_model
self.top_down_pyramid_size = top_down_pyramid_size
self.post_nms_rois_training = post_nms_rois_training
self.post_nms_rois_inference = post_nms_rois_inference
self.pre_nms_limit = pre_nms_limit
self.rpn_nms_threshold = rpn_nms_threshold
self.use_rpn_rois = use_rpn_rois
self.model_dir = model_dir
self.optimizer_method = optimizer_method
self.learning_rate = learning_rate
self.momentum = momentum
self.weight_decay = weight_decay
self.image_min_dim = image_min_dim
self.image_max_dim = image_max_dim
self.image_min_scale = image_min_scale
self.image_resize_mode = image_resize_mode
self.max_gt_instances = max_gt_instances
self.rpn_train_anchors_per_image = rpn_train_anchors_per_image
self.image_meta_size = 1 + 3 + 3 + 4 + 1 + self.num_classes
self.reuse = False
self._anchor_cache = {}
self.batch_size = self.gpu_count * self.image_per_gpu
self.backbone_shape = utils.compute_backbone_shapes(
self.backbone, self.backbone_strides, self.image_shape)
self.num_anchors_per_image = len(self.rpn_anchor_ratios) * (
self.backbone_shape[0][0] * self.backbone_shape[0][0] +
self.backbone_shape[1][0] * self.backbone_shape[1][0] +
self.backbone_shape[2][0] * self.backbone_shape[2][0] +
self.backbone_shape[3][0] * self.backbone_shape[3][0] +
self.backbone_shape[4][0] * self.backbone_shape[4][0])
with self.graph.as_default():
self.is_training = tf.placeholder_with_default(False, [])
self.input_image = tf.placeholder(dtype=tf.float32,
shape=[
None, self.image_shape[0],
self.image_shape[1],
self.image_shape[2]
],
name='input_image')
self.input_image_meta = tf.placeholder(
dtype=tf.int32,
shape=[None, self.image_meta_size],
name='input_image_meta')
if mode == 'training':
self.input_rpn_match = tf.placeholder(
dtype=tf.int32,
shape=[None, self.num_anchors_per_image, 1],
name='input_rpn_match')
self.input_rpn_boxes = tf.placeholder(
dtype=tf.float32,
shape=[None, self.rpn_train_anchors_per_image, 4],
name='input_rpn_boxes')
self.input_gt_class_ids = tf.placeholder(
dtype=tf.int32,
shape=[None, self.max_gt_instances],
name='input_gt_class_ids')
self.input_gt_boxes = tf.placeholder(
dtype=tf.float32,
shape=[None, self.max_gt_instances, 4],
name='input_gt_boxes')
self.input_gt_boxes_normalized = utils.norm_boxes_graph(
self.input_gt_boxes,
tf.shape(self.input_image)[1:3])
self.proposal_count = self.post_nms_rois_training
if self.use_mini_mask:
self.input_gt_masks = tf.placeholder(
dtype=tf.bool,
shape=[
None, self.mini_mask_shape[0],
self.mini_mask_shape[1], self.max_gt_instances
],
name='input_gt_mask')
else:
self.input_gt_masks = tf.placeholder(
dtype=tf.bool,
shape=[
None, self.image_shape[0], self.image_shape[1],
self.max_gt_instances
],
name='input_gt_mask')
elif mode == 'inference':
self.input_anchors = tf.placeholder(dtype=tf.float32,
shape=[None, None, 4],
name='input_anchors')
self.proposal_count = self.post_nms_rois_inference
self.resnet = Resnet(name='resnet',
architecture=self.backbone,
is_training=self.is_training,
stage5=self.stage5,
use_bias=self.use_bias)
arg_scope = nets.resnet_v2.resnet_arg_scope()
with slim.arg_scope(arg_scope):
_, self.end_points = nets.resnet_v2.resnet_v2_50(
self.input_image,
num_classes=None,
is_training=self.is_training)
self.fpn = FPN(name='fpn',
top_down_pyramid_size=self.top_down_pyramid_size,
use_bias=self.use_bias)
self.rpn = RPN(name='rpn',
anchors_per_location=len(self.rpn_anchor_ratios),
anchor_stride=self.rpn_anchor_stride,
is_training=self.is_training,
use_bias=self.use_bias)
self.proposal = ProposalLayer(self.pre_nms_limit,
self.proposal_count,
self.rpn_nms_threshold,
self.image_per_gpu)
self.pyramidRoiPooling = PyramidRoiPooling(
name='PyramidRoiPooling', roi_size=self.roi_size)
self.objDetection = ObjDetection(
image_per_gpu=self.image_per_gpu,
gpu_count=self.gpu_count,
detection_max_instances=self.detection_max_instances)
self.targetDetection = TargetDetection(
mask_shape=self.mask_shape,
image_per_gpu=self.image_per_gpu,
train_rois_per_image=self.train_rois_per_image)
self.fpnClassifier = FpnClassifier('FpnClassifier',
pool_size=self.pool_size,
num_classes=self.num_classes,
is_training=self.is_training)
self.fpnMask = FpnMask('FpnMask',
num_classes=self.num_classes,
is_training=self.is_training)
def __init__(self):
super(DPNet, self).__init__()
resnet = Resnet()
self.layer0 = resnet.layer0
self.layer1 = resnet.layer1
self.layer2 = resnet.layer2
self.layer3 = resnet.layer3
self.layer4 = resnet.layer4
self.nlb_paramid1 = DPM(256, sub_sample=False)
self.nlb_paramid2 = DPM(256, sub_sample=False)
self.reduce_layer4 = nn.Sequential(
nn.Conv2d(2048, 256, kernel_size=1),
nn.BatchNorm2d(256),
nn.PReLU(),
)
self.reduce_layer3 = nn.Sequential(
nn.Conv2d(1024, 256, kernel_size=1),
nn.BatchNorm2d(256),
nn.PReLU(),
)
self.reduce_layer2 = nn.Sequential(
nn.Conv2d(512, 256, kernel_size=1),
nn.BatchNorm2d(256),
nn.PReLU(),
)
self.reduce_layer1 = nn.Sequential(
nn.Conv2d(256, 256, kernel_size=1),
nn.BatchNorm2d(256),
nn.PReLU(),
)
self.predict_dnlp1 = nn.Sequential(
nn.Conv2d(256, 64, kernel_size=3, padding=1), nn.BatchNorm2d(64),
nn.PReLU(), nn.Conv2d(64, 64, kernel_size=3, padding=1),
nn.BatchNorm2d(64), nn.PReLU(), nn.Conv2d(64, 1, kernel_size=1))
self.predict4 = nn.Sequential(
nn.Conv2d(257, 64, kernel_size=3, padding=1), nn.BatchNorm2d(64),
nn.PReLU(), nn.Conv2d(64, 64, kernel_size=3, padding=1),
nn.BatchNorm2d(64), nn.PReLU(), nn.Conv2d(64, 1, kernel_size=1))
self.predict3 = nn.Sequential(
nn.Conv2d(257, 64, kernel_size=3, padding=1), nn.BatchNorm2d(64),
nn.PReLU(), nn.Conv2d(64, 64, kernel_size=3, padding=1),
nn.BatchNorm2d(64), nn.PReLU(), nn.Conv2d(64, 1, kernel_size=1))
self.predict2 = nn.Sequential(
nn.Conv2d(257, 64, kernel_size=3, padding=1), nn.BatchNorm2d(64),
nn.PReLU(), nn.Conv2d(64, 64, kernel_size=3, padding=1),
nn.BatchNorm2d(64), nn.PReLU(), nn.Conv2d(64, 1, kernel_size=1))
self.predict1 = nn.Sequential(
nn.Conv2d(257, 64, kernel_size=3, padding=1), nn.BatchNorm2d(64),
nn.PReLU(), nn.Conv2d(64, 64, kernel_size=3, padding=1),
nn.BatchNorm2d(64), nn.PReLU(), nn.Conv2d(64, 1, kernel_size=1))
for m in self.modules():
if isinstance(m, nn.ReLU) or isinstance(m, nn.Dropout):
m.inplace = True
#loading the training and the test data
X_train,Y_train,X_test,Y_test,classes=load_dataset()
num_classes=len(classes)
x1,y1,c1=X_train.shape
# defining placeholder
X=tf.placeholder(tf.float32,[None,x1,y1,c1])
Y=tf.placeholder(tf.float32,[None,num_classes])
#making dataset iterator
ds=Dataset.from_tensor_slices((X,Y)).batch(BATCH_SIZE).repeat()
iterator=tf.make_initializable_iterator()
sess.run(iterator.initializer,feed_dict={X:X_train,Y:Y_train})
batch_x,batch_y=iterator.get_next()
Y_pred=Resnet(batch_x,num_classes)
loss_op=train_op(Y_pred,batch_y)
optimizer-train_op(loss,learning_rate):
accuracy=tf.reduce_mean(tf.cast(tf.equal(tf.argmax(Y_pred,1),tf.argmax(Y_pred,1)),tf.float32))
init=tf.global_variables_initializer()
sess.run(init)
num_batches=X_train.shape[0]/BATCH_SIZE
for epoch in num_epochs:
for _ in num_batches:
_,accuracy,loss,=sess.run([optimizer,accuracy,loss])
if epoch%2==0:
print('Accuracy after {1} epoch is {0} '.format(accuracy,epoch))
aug_train = Augmentation(x_train, y_train, 14400)
x_train, y_train = aug_train.data_augmentation()
print('after augmentation shape')
print(x_train.shape, x_test.shape)
#feature_train = FeatureExtraction(x_train)
#feature_test = FeatureExtraction(x_test)
#gray = feature_train.to_grayscale()
#sat = feature_train.get_color_sat().reshape(-1,1)
#pix = feature_train.get_color_pix_r().reshape(-1,1)
#grad = feature_train.get_img_gradient()
#print(gray.shape, sat.shape, pix.shape, grad.shape)
#x_train = np.concatenate((feature_train.to_grayscale(), feature_train.get_color_sat().reshape(-1,1), feature_train.get_color_pix_r().reshape(-1,1), feature_train.get_img_gradient()),axis = 1)
#x_test = np.concatenate((feature_test.to_grayscale(), feature_test.get_color_sat().reshape(-1,1), feature_test.get_color_pix_r().reshape(-1,1), feature_test.get_img_gradient()),axis = 1)
#print(x_train.shape)
#print(np.concatenate((gray, sat, pix), axis =1).shape)
#x_train = np.concatenate((gray, grad, sat, pix), axis =1)
#print('after data engineering x_train shape, x_test shape')
#print(x_train.shape, x_test.shape)
#x_train, x_test = data_eng.to_standardize(x_train, x_test)
#print('std done')
#x_train,x_test = data_eng.to_PCA(x_train, x_test)
#print('pca done')
res = Resnet(x_train, x_test, y_train, y_test)
accurate = res.train()
print(accurate)
# Main from resnet import Resnet import numpy as np data = np.array([[0, 1, 1], [1, 0, 0], [1, 1, 1]]) # Example test dataset layers_count = 3 # The number of layers in the resnet node_count = 3 # The number of nodes in each layer resnet = Resnet(data, layers_count, node_count) # Initialize a resnet resnet.train()
def init_model(args):
source_train_loader = get_loader(name_dataset=args.source,
batch_size=args.batch_size,
train=True)
target_train_loader = get_loader(name_dataset=args.target,
batch_size=args.batch_size,
train=True)
source_evaluate_loader = get_loader(name_dataset=args.source,
batch_size=args.batch_size,
train=False)
target_evaluate_loader = get_loader(name_dataset=args.target,
batch_size=args.batch_size,
train=False)
n_classes = len(source_train_loader.dataset.classes)
# ~ Paper : "We initialized the other layers with the parameters pre-trained on ImageNet"
# check https://github.com/pytorch/vision/blob/master/torchvision/models/alexnet.py
model = Resnet(31)
# ~ Paper : The dimension of last fully connected layer (fc8) was set to the number of categories (31)
# model.classifier[6] = nn.Linear(4096, n_classes)
# # ~ Paper : and initialized with N(0, 0.005)
# torch.nn.init.normal_(model.classifier[6].weight, mean=0, std=5e-3)
#
# # Initialize bias to small constant number (http://cs231n.github.io/neural-networks-2/#init)
# model.classifier[6].bias.data.fill_(0.01)
model = model.to(device=args.device)
# ~ Paper : "The learning rate of fc8 is set to 10 times the other layers as it was training from scratch."
# optimizer = torch.optim.SGD([
# # {'params': model.features.parameters()},
# # {'params': model.classifier[:6].parameters()},
# # # fc8 -> 7th element (index 6) in the Sequential block
# {'params': model.classifier[6].parameters(), 'lr': 10 * args.lr}
# ], lr=args.lr, momentum=args.momentum) # if not specified, the default lr is used
optimizer = torch.optim.SGD(
[
{
'params': model.base_network.parameters()
},
# {'params': model.bottleneck_layer.parameters(), 'lr': 10 * CFG['lr']},
{
'params': model.classifier_layer.parameters(),
'lr': 10 * args.lr
},
],
lr=args.lr,
momentum=args.momentum,
weight_decay=5e-4)
tracker = Tracker()
for i in range(args.epochs):
train(model, optimizer, source_train_loader, target_train_loader,
tracker, args, i)
evaluate(model, source_evaluate_loader, 'source', tracker, args, i)
evaluate(model, target_evaluate_loader, 'target', tracker, args, i)
# Save logged classification loss, coral loss, source accuracy, target accuracy
torch.save(tracker.to_dict(), args.da_loss + "_log.pth")
print("Final Evaluation\r")
return evaluate(model, target_evaluate_loader, 'target', tracker, args, i)
elif args.model_type == 'ex_gradcam2':
model = VGG_interpretable_gradcam2(num_classes=num_classe)
else:
model = VGGNet(num_classes=num_classe)
#model = VGG_gradcam(num_classes=num_classe)
elif args.model == 'resnet':
if args.model_type == 'ex_atten':
model = VGG_interpretable_atten(num_classes=num_classe)
elif args.model_type == 'ex':
model = Resnet_interpretable(num_classes=num_classe)
elif args.model_type == 'ex_gradcam':
model = Resnet_interpretable_gradcam(num_classes=num_classe)
elif args.model_type == 'ex_gradcam2':
model = VGG_interpretable_gradcam2(num_classes=num_classe)
else:
model = Resnet(num_classes=num_classe)
elif args.model == 'mobilenet':
if args.model_type == 'ex_atten':
model = VGG_interpretable_atten(num_classes=num_classe)
elif args.model_type == 'ex':
model = VGG_interpretable(num_classes=num_classe)
elif args.model_type == 'ex_gradcam':
model = Mobile_interpretable_gradcam(num_classes=num_classe)
elif args.model_type == 'ex_gradcam2':
model = VGG_interpretable_gradcam2(num_classes=num_classe)
else:
model = MobileNet(num_classes=num_classe)
elif args.model == 'alexnet':
if args.model_type == 'ex_atten':
model = VGG_interpretable_atten(num_classes=num_classe)
elif args.model_type == 'ex':
def predict_test(name='lung',
mode='test',
seg_model_path=SEG_LUNG_TRAIN_WEIGHT,
class_model_path=CLASS_LUNG_TRAIN_WEIGHT,
seg_thresh_hold=0.8,
limit=[0, 0]):
detect_net = UNet()
class_net = Resnet()
detect_model = detect_net.get_model(0.1)
detect_model.load_weights(seg_model_path)
class_model = class_net.get_model(0.1)
class_model.load_weights(class_model_path)
columns = [
'seriesuid', 'coordX', 'coordY', 'coordZ', 'class', 'probability'
]
df = pd.DataFrame(columns=columns)
for img, meta in get_files(name, mode):
count = 0
cubs = []
cub_sizes = []
for w in range(limit[0], img.shape[0] - limit[0], 32):
for h in range(limit[1], img.shape[1] - limit[1], 32):
for d in range(0, img.shape[2], 32):
if d + INPUT_DEPTH > img.shape[2]:
d = img.shape[2] - INPUT_DEPTH
if h + INPUT_HEIGHT > img.shape[1]:
h = img.shape[1] - INPUT_HEIGHT
if w + INPUT_WIDTH > img.shape[0]:
w = img.shape[0] - INPUT_WIDTH
cub = img[w:w + INPUT_WIDTH, h:h + INPUT_HEIGHT,
d:d + INPUT_DEPTH]
if np.all(cub == ZERO_CENTER):
continue
#batch_cub = cub[np.newaxis, ..., np.newaxis]
cubs.append(cub)
cub_sizes.append([w, h, d])
for k in range(0, len(cub_sizes), 16):
t = 16
if k + 16 >= len(cub_sizes):
t = len(cub_sizes) - k
batch_cub = np.array(cubs[k:t + k])
batch_cub_sizes = cub_sizes[k:t + k]
batch_cub = batch_cub[..., np.newaxis]
pre_y_batch = detect_model.predict(batch_cub)
for k in range(pre_y_batch.shape[0]):
pre_y = pre_y_batch[k, :, :, :, 0] > seg_thresh_hold
#print('predicted pix:'+ str(np.sum(pre_y)))
if np.sum(pre_y) > 0:
crops, crop_centers, diameter, bboxes = crop_for_class(
img, pre_y, np.array(batch_cub_sizes[k]))
#print('find:'+str(len(crop_centers)))
for i, center in enumerate(crop_centers):
crop = crops[i]
crop_cub = crop[np.newaxis, ..., np.newaxis]
class_type = class_model.predict(crop_cub)
class_type = class_type[0]
index = np.argmax(class_type)
if index > 0:
#print('Add one')
location = meta['origin'] + center
new_row = pd.DataFrame([[
meta['seriesuid'], location[0], location[1],
location[2], label_softmax_reverse[index],
class_type[index]
]],
columns=columns)
df = df.append(new_row, ignore_index=True)
df.to_csv('./output/predict_' + name + '_' + mode + '.csv',
index=False)
print('finished')
else:
continue_training = False
for optimizer in optim_array:
for p_value in p_values:
print('-'*40, optimizer, '-'*40)
op = optim_params[optimizer]
op['lr'] = op['lr']/(10**i)
if optimizer == 'adamw' and dataset=='imagenet':
op['weight_decay'] = 0.05
if optimizer is not 'adamw':
model = Resnet(data_format='channels_last', classes=hp['classes'], wt_decay = op['weight_decay'])
else:
model = Resnet(data_format='channels_last', classes=hp['classes'], wt_decay = 0)
model._set_inputs(tf.zeros((batch_size, 32, 32, 3)))
learning_rate = tf.train.exponential_decay(op['lr'], tf.train.get_global_step() * batch_size,
hp['decay_after']*train_size, 0.1, staircase=True)
logfile = 'log_'+str(p_value)+ '_' + dataset +'.csv'
if(continue_training):
load_model_filepath = 'model_'+str(p_value)+'_' + dataset + '_epochs'+ str(continue_epoch)+'.h5'
save_model_filepath = 'model_'+str(p_value)+'_' + dataset + '_epochs'+ str(continue_epoch+epochs)+'.h5'
model = load_model(load_model_filepath, model)
else:
def test(model_path='model/model-30000'):
video_dir = os.path.join(parentUrl, 'data', 'train', 'lab')
box_to_vect_dataset = BoxToVectDataSet(
train_set_file='data/train.npy',
val_set_file='data/val.npy',
video_files=[
os.path.join(video_dir, '4p-c0.avi'),
os.path.join(video_dir, '4p-c1.avi'),
os.path.join(video_dir, '4p-c2.avi'),
os.path.join(video_dir, '4p-c3.avi'),
],
test_set_file='data/test.npy',
image_width=Config['image_width'],
image_height=Config['image_height'])
box_to_vect = Resnet(
image_height=Config['image_height'],
image_width=Config['image_width'],
vector_dim=128,
alpha=Config['alpha'],
feature_map_layer='block_layer3',
resnet_size=18,
data_format='channels_first',
mode='test',
init_learning_rate=0.001,
optimizer_name='adam',
batch_size=Config['batch_size'],
model_path='model/',
logdir='log/',
)
sess = tf.Session()
saver = tf.train.Saver()
saver.restore(sess, model_path)
print('Load weights form', model_path)
max_ap = 0
min_an = 100
for _ in range(100):
image_batch, box_batch, box_ind_batch = box_to_vect_dataset.get_data_batch(
batch_size=Config['batch_size'], split='test')
embedding = box_to_vect.inference(image_batch, box_batch,
box_ind_batch, sess)
embedding = np.reshape(embedding, [-1, 3, embedding.shape[-1]])
anchor, positive, negative = embedding[:,
0, :], embedding[:,
1, :], embedding[:,
2, :]
# print('anchor\n', anchor)
# print('positive\n', positive)
# print('negative\n', negative)
a_p_squared = np.sqrt(np.sum(np.square(anchor - positive), axis=1))
a_n_squared = np.sqrt(np.sum(np.square(anchor - negative), axis=1))
print('-' * 50)
# print('a_p_squared:\n', a_p_squared)
# print('a_n_squared:\n', a_n_squared)
a_p_squared_max = np.max(a_p_squared)
a_n_squared_min = np.min(a_n_squared)
print('a_p_squared_max:', a_p_squared_max)
print('a_n_squared_min:', a_n_squared_min)
# print('diff:\n', a_p_squared-a_n_squared)
if max_ap < a_p_squared_max:
max_ap = a_p_squared_max
if min_an > a_n_squared_min:
min_an = a_n_squared_min
print('max_ap', max_ap)
print('min_an', min_an)