def model(self):
encoded_input = Input(shape=(128,))
hidden_layer = Dense(self.conf_s.NUMBER_OF_NEURONS_IN_HIDDEN_LAYER, activation='sigmoid')(encoded_input)
output_layer = Dense(conf.NUM_LABELS, activation='sigmoid')(hidden_layer)
classifier = Model(input=encoded_input, output=output_layer)
classifier.compile(self.conf_s.OPTIMIZER, loss='categorical_crossentropy')
return classifier
def test1():
seq_size = 10
batch_size = 10
rnn_size = 1
xin = Input(batch_shape=(batch_size, seq_size,1))
xtop = Input(batch_shape=(batch_size, seq_size))
xbranch, xsummary = RTTN(rnn_size, return_sequences=True)([xin, xtop])
model = Model(input=[xin, xtop], output=[xbranch, xsummary])
model.compile(loss='MSE', optimizer='SGD')
data_gen = generate_data_batch(batch_size, seq_size)
model.fit_generator(generator=data_gen, samples_per_epoch=1000, nb_epoch=100)
def nn_architecture_seg_3d(input_shape, pool_size=(2, 2, 2), n_labels=1, initial_learning_rate=0.00001,
depth=3, n_base_filters=16, metrics=dice_coefficient, batch_normalization=True):
inputs = Input(input_shape)
current_layer = inputs
levels = list()
for layer_depth in range(depth):
layer1 = create_convolution_block(input_layer=current_layer, n_filters=n_base_filters * (2**layer_depth),
batch_normalization=batch_normalization)
layer2 = create_convolution_block(input_layer=layer1, n_filters=n_base_filters * (2**layer_depth) * 2,
batch_normalization=batch_normalization)
if layer_depth < depth - 1:
current_layer = MaxPooling3D(pool_size=pool_size)(layer2)
levels.append([layer1, layer2, current_layer])
else:
current_layer = layer2
levels.append([layer1, layer2])
for layer_depth in range(depth - 2, -1, -1):
up_convolution = UpSampling3D(size=pool_size)
concat = concatenate([up_convolution, levels[layer_depth][1]], axis=1)
current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=concat, batch_normalization=batch_normalization)
current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=current_layer,
batch_normalization=batch_normalization)
final_convolution = Conv3D(n_labels, (1, 1, 1))(current_layer)
act = Activation('sigmoid')(final_convolution)
model = Model(inputs=inputs, outputs=act)
if not isinstance(metrics, list):
metrics = [metrics]
model.compile(optimizer=Adam(lr=initial_learning_rate), loss=dice_coefficient_loss, metrics=metrics)
return model
class FergusNModel(object):
def __init__(self, igor):
now = datetime.now()
self.run_name = "fergusn_{}mo_{}day_{}hr_{}min".format(
now.month, now.day, now.hour, now.minute)
log_location = join(igor.log_dir, self.run_name + ".log")
self.logger = igor.logger = make_logger(igor, log_location)
igor.verify_directories()
self.igor = igor
@classmethod
def from_yaml(cls, yamlfile, kwargs=None):
igor = Igor.from_file(yamlfile)
igor.prep()
model = cls(igor)
model.make(kwargs)
return model
@classmethod
def from_config(cls, config, kwargs=None):
igor = Igor(config)
model = cls(igor)
igor.prep()
model.make(kwargs)
return model
def load_checkpoint_weights(self):
weight_file = join(self.igor.model_location, self.igor.saving_prefix,
self.igor.checkpoint_weights)
if exists(weight_file):
self.logger.info("+ Loading checkpoint weights")
self.model.load_weights(weight_file, by_name=True)
else:
self.logger.warning(
"- Checkpoint weights do not exist; {}".format(weight_file))
def plot(self):
filename = join(self.igor.model_location, self.igor.saving_prefix,
'model_visualization.png')
kplot(self.model, to_file=filename)
self.logger.debug("+ Model visualized at {}".format(filename))
def make(self, theano_kwargs=None):
'''Make the model and compile it.
Igor's config options control everything.
Arg:
theano_kwargs as dict for debugging theano or submitting something custom
'''
if self.igor.embedding_type == "convolutional":
make_convolutional_embedding(self.igor)
elif self.igor.embedding_type == "token":
make_token_embedding(self.igor)
elif self.igor.embedding_type == "shallowconv":
make_shallow_convolutional_embedding(self.igor)
elif self.igor.embedding_type == "minimaltoken":
make_minimal_token_embedding(self.igor)
else:
raise Exception("Incorrect embedding type")
B = self.igor.batch_size
spine_input_shape = (B, self.igor.max_num_supertags)
child_input_shape = (B, 1)
parent_input_shape = (B, 1)
E, V = self.igor.word_embedding_size, self.igor.word_vocab_size # for word embeddings
repeat_N = self.igor.max_num_supertags # for lex
mlp_size = self.igor.mlp_size
## dropout parameters
p_emb = self.igor.p_emb_dropout
p_W = self.igor.p_W_dropout
p_U = self.igor.p_U_dropout
w_decay = self.igor.weight_decay
p_mlp = self.igor.p_mlp_dropout
def predict_params():
return {
'output_dim': 1,
'W_regularizer': l2(w_decay),
'activation': 'relu',
'b_regularizer': l2(w_decay)
}
dspineset_in = Input(batch_shape=spine_input_shape,
name='daughter_spineset_in',
dtype='int32')
pspineset_in = Input(batch_shape=spine_input_shape,
name='parent_spineset_in',
dtype='int32')
dhead_in = Input(batch_shape=child_input_shape,
name='daughter_head_input',
dtype='int32')
phead_in = Input(batch_shape=parent_input_shape,
name='parent_head_input',
dtype='int32')
dspine_in = Input(batch_shape=child_input_shape,
name='daughter_spine_input',
dtype='int32')
inputs = [dspineset_in, pspineset_in, dhead_in, phead_in, dspine_in]
### Layer functions
############# Convert the word indices to vectors
F_embedword = Embedding(input_dim=V,
output_dim=E,
mask_zero=True,
W_regularizer=l2(w_decay),
dropout=p_emb)
if self.igor.saved_embeddings is not None:
self.logger.info("+ Cached embeddings loaded")
F_embedword.initial_weights = [self.igor.saved_embeddings]
###### Prediction Functions
## these functions learn a vector which turns a tensor into a matrix of probabilities
### P(Parent supertag | Child, Context)
F_parent_predict = ProbabilityTensor(
name='parent_predictions',
dense_function=Dense(**predict_params()))
### P(Leaf supertag)
F_leaf_predict = ProbabilityTensor(
name='leaf_predictions', dense_function=Dense(**predict_params()))
###### Network functions.
##### Input word, correct its dimensions (basically squash in a certain way)
F_singleword = compose(Fix(), F_embedword)
##### Input spine, correct diemnsions, broadcast across 1st dimension
F_singlespine = compose(RepeatVector(repeat_N), Fix(),
self.igor.F_embedspine)
##### Concatenate and map to a single space
F_alignlex = compose(
RepeatVector(repeat_N), Dropout(p_mlp),
Dense(mlp_size, activation='relu', name='dense_align_lex'), concat)
F_alignall = compose(
Distribute(Dropout(p_mlp), name='distribute_align_all_dropout'),
Distribute(Dense(mlp_size,
activation='relu',
name='align_all_dense'),
name='distribute_align_all_dense'), concat)
F_alignleaf = compose(
Distribute(
Dropout(p_mlp * 0.66), name='distribute_leaf_dropout'
), ### need a separate oen because the 'concat' is different for the two situations
Distribute(Dense(mlp_size, activation='relu', name='leaf_dense'),
name='distribute_leaf_dense'),
concat)
### embed and form all of the inputs into their components
### note: spines == supertags. early word choice, haven't refactored.
leaf_spines = self.igor.F_embedspine(dspineset_in)
pspine_context = self.igor.F_embedspine(pspineset_in)
dspine_single = F_singlespine(dspine_in)
dhead = F_singleword(dhead_in)
phead = F_singleword(phead_in)
### combine the lexical material
lexical_context = F_alignlex([dhead, phead])
#### P(Parent Supertag | Daughter Supertag, Lexical Context)
### we know the daughter spine, want to know the parent spine
### size is (batch, num_supertags)
parent_problem = F_alignall(
[lexical_context, dspine_single, pspine_context])
### we don't have the parent, we just have a leaf
leaf_problem = F_alignleaf([lexical_context, leaf_spines])
parent_predictions = F_parent_predict(parent_problem)
leaf_predictions = F_leaf_predict(leaf_problem)
predictions = [parent_predictions, leaf_predictions]
theano_kwargs = theano_kwargs or {}
## make it quick so i can load in the weights.
self.model = Model(input=inputs,
output=predictions,
preloaded_data=self.igor.preloaded_data,
**theano_kwargs)
#mask_cache = traverse_nodes(parent_prediction)
#desired_masks = ['merge_3.in.mask.0']
#self.p_tensor = K.function(inputs+[K.learning_phase()], [parent_predictions, F_parent_predict.inbound_nodes[0].input_masks[0]])
if self.igor.from_checkpoint:
self.load_checkpoint_weights()
elif not self.igor.in_training:
raise Exception("No point in running this without trained weights")
if not self.igor.in_training:
expanded_children = RepeatVector(repeat_N, axis=2)(leaf_spines)
expanded_parent = RepeatVector(repeat_N, axis=1)(pspine_context)
expanded_lex = RepeatVector(repeat_N, axis=1)(
lexical_context
) # axis here is arbitary; its repeating on 1 and 2, but already repeated once
huge_tensor = concat(
[expanded_lex, expanded_children, expanded_parent])
densely_aligned = LastDimDistribute(
F_alignall.get(1).layer)(huge_tensor)
output_predictions = Distribute(
F_parent_predict, force_reshape=True)(densely_aligned)
primary_inputs = [phead_in, dhead_in, pspineset_in, dspineset_in]
leaf_inputs = [phead_in, dhead_in, dspineset_in]
self.logger.info("+ Compiling prediction functions")
self.inner_func = K.Function(primary_inputs + [K.learning_phase()],
output_predictions)
self.leaf_func = K.Function(leaf_inputs + [K.learning_phase()],
leaf_predictions)
try:
self.get_ptensor = K.function(
primary_inputs + [K.learning_phase()], [
output_predictions,
])
except:
import pdb
pdb.set_trace()
else:
optimizer = Adam(self.igor.LR,
clipnorm=self.igor.max_grad_norm,
clipvalue=self.igor.grad_clip_threshold)
theano_kwargs = theano_kwargs or {}
self.model.compile(loss="categorical_crossentropy",
optimizer=optimizer,
metrics=['accuracy'],
**theano_kwargs)
#self.model.save("here.h5")
def likelihood_function(self, inputs):
if self.igor.in_training:
raise Exception("Not in testing mode; please fix the config file")
return self.inner_func(tuple(inputs) + (0., ))
def leaf_function(self, inputs):
if self.igor.in_training:
raise Exception("Not in testing mode; please fix the config file")
return self.leaf_func(tuple(inputs) + (0., ))
def train(self):
replacers = {
"daughter_predictions": "child",
"parent_predictions": "parent",
"leaf_predictions": "leaf"
}
train_data = self.igor.train_gen(forever=True)
dev_data = self.igor.dev_gen(forever=True)
N = self.igor.num_train_samples
E = self.igor.num_epochs
# generator, samplers per epoch, number epochs
callbacks = [ProgbarV2(3, 10, replacers=replacers)]
checkpoint_fp = join(self.igor.model_location, self.igor.saving_prefix,
self.igor.checkpoint_weights)
self.logger.info("+ Model Checkpoint: {}".format(checkpoint_fp))
callbacks += [
ModelCheckpoint(filepath=checkpoint_fp,
verbose=1,
save_best_only=True)
]
callbacks += [LearningRateScheduler(lambda epoch: self.igor.LR * 0.9)]
csv_location = join(self.igor.log_dir, self.run_name + ".csv")
callbacks += [CSVLogger(csv_location)]
self.model.fit_generator(generator=train_data,
samples_per_epoch=N,
nb_epoch=E,
callbacks=callbacks,
verbose=1,
validation_data=dev_data,
nb_val_samples=self.igor.num_dev_samples)
def debug(self):
dev_data = self.igor.dev_gen(forever=False)
X, Y = next(dev_data)
self.model.predict_on_batch(X)
#self.model.evaluate_generator(dev_data, self.igor.num_dev_samples)
def profile(self, num_iterations=1):
train_data = self.igor.train_gen(forever=True)
dev_data = self.igor.dev_gen(forever=True)
# generator, samplers per epoch, number epochs
callbacks = [ProgbarV2(1, 10)]
self.logger.debug("+ Beginning the generator")
self.model.fit_generator(generator=train_data,
samples_per_epoch=self.igor.batch_size * 10,
nb_epoch=num_iterations,
callbacks=callbacks,
verbose=1,
validation_data=dev_data,
nb_val_samples=self.igor.batch_size)
self.logger.debug(
"+ Calling theano's pydot print.. this might take a while")
theano.printing.pydotprint(self.model.train_function.function,
outfile='theano_graph.png',
var_with_name_simple=True,
with_ids=True)
self.logger.debug("+ Calling keras' print.. this might take a while")
self.plot("keras_graph.png")
def gru_model(embedding_weights, cv_dat, max_len, model_w, lda, dictionary,
idx2word, alpha, gru_time_steps):
"""
GRU with attention mechanism
:param embedding_weights:
:param cv_dat:
:param max_len:
:param model_w:
:param lda:
:param dictionary:
:param idx2word:
:param alpha:
:return:
"""
max_len = 200 if max_len > 1000 else max_len
#max_len = 1000
dropout = 0.8
print max_len
#json_file = open(model_w+'model.json', 'r')
#loaded_model_json = json_file.read()
#json_file.close()
#model_lda = model_from_json(loaded_model_json)
# load weights into new model
#layer_dict = dict([(layer.name, layer) for layer in model_lda.layers])
#print layer_dict.keys()
##print layer_dict
train_x, test_x, train_y, test_y = cv_dat
#test_lda = get_alpha(test_x, lda, dictionary, idx2word)
print "Maximum length of sentence:" + str(max_len)
print "Distribution of labels in training set:"
print Counter([np.argmax(dat) for dat in train_y])
print "Distribution of labels in testing set:"
print Counter([np.argmax(dat) for dat in test_y])
#print "Distribution of labels in testing set 1k:"
#print Counter([np.argmax(dat) for dat in test_y1k])
#print (train_x.shape)
#print train_y.shape
train_x, val_x, train_y, val_y = train_test_split(train_x,
train_y,
test_size=0.166667,
random_state=666,
stratify=train_y)
train_lda = get_alpha(train_x, lda, dictionary, idx2word, max_len)
val_lda = get_alpha(val_x, lda, dictionary, idx2word, max_len)
print val_lda[0]
test_lda = get_alpha(test_x, lda, dictionary, idx2word, max_len)
#test_lda1k = get_alpha(test_x1k, lda, dictionary, idx2word, max_len)
print val_lda.shape
#defining the model architecture now
train_x = np.array(sequence.pad_sequences(train_x, maxlen=max_len),
dtype=np.int)
val_x = np.array(sequence.pad_sequences(val_x, maxlen=max_len),
dtype=np.int)
test_x = np.array(sequence.pad_sequences(test_x, maxlen=max_len),
dtype=np.int)
#test_x1k = np.array(sequence.pad_sequences(test_x1k, maxlen=max_len), dtype=np.int)
review_text = Input(shape=(max_len, ), dtype='int64', name="body_input")
lda_input = Input(shape=(50, ), dtype='float32', name="lda_inp")
embedded_layer_body = Embedding(embedding_weights.shape[0],
embedding_weights.shape[1],
mask_zero=False,
input_length=max_len,
weights=[embedding_weights],
trainable=True)(review_text)
#define the GRU with attention
#gru_l = LSTMCustom(gru_time_steps, init='glorot_uniform', activation='tanh',dropout_W=0.3, dropout_U=0.3, topic_distribution=lda_input)(embedded_layer_body)
gru_l = LSTM(gru_time_steps,
init='glorot_uniform',
activation='tanh',
dropout_W=0.3,
dropout_U=0.3)(embedded_layer_body)
print gru_l
#gru_lda = merge([gru_l, lda_input], name='add_lda', mode='sum')
#gru_lda = Lambda(lambda x: merge([x, lda_input], name='add_lda', mode='sum'))(gru_l)
#attn_wghts = Permute((2, 1))(gru_lda)
#print attn_wghts
#ttn_wghts = Reshape((300, gru_time_steps))(attn_wghts)
#attn_wghts = Dense(gru_time_steps, activation='softmax')(attn_wghts)
#alpha_wghts = Permute((2, 1), name='attention_vec')(attn_wghts)
#output_attention_mul = merge([attn_wghts, alpha_wghts], name='attention_mul', mode='mul')
#attention_mul = Lambda(lambda x: K.sum(x, axis=1))(output_attention_mul)
#add_lda = merge([attention_mul, lda_input], name='add_lda', mode='sum')
#print attention_mul
#l_dense = TimeDistributed(Dense(gru_time_steps*2))(gru_l)
#l_att = Attention(lda=lda_input)(gru_l)
#output_lda = Dense(30, activation='softmax', name='out_lda')(attention_mul)
hidden_layer = Dense(1200,
activation='tanh',
kernel_initializer="glorot_uniform")(gru_l)
#hidden_concat = concatenate([hidden_layer, lda_vec])
dropout_hidden = Dropout(dropout)(hidden_layer)
#merge_hidden = concatenate([dropout_hidden, lda_input])
batch_norm = BatchNormalization()(dropout_hidden)
hidden_layer_3 = Dense(600,
activation='tanh',
kernel_initializer="glorot_uniform")(batch_norm)
dropout_hidden_3 = Dropout(0.5)(hidden_layer_3)
batch_n_3 = BatchNormalization()(dropout_hidden_3)
output_layer = Dense(2, activation='softmax', name='out_sent')(batch_n_3)
model = Model([review_text, lda_input], output=[output_layer])
layer_dict_nu = dict([(layer.name, layer) for layer in model.layers])
adam = Adam(lr=0.0001)
#model.compile(loss='categorical_crossentropy', optimizer=adam, metrics=['accuracy'], loss_weights={'out_sent': (1 - alpha), 'out_lda': alpha})
model.compile(loss='categorical_crossentropy',
optimizer=adam,
metrics=['accuracy'])
#model.compile(loss=ncce, optimizer=adam, metrics=['accuracy'])
earlystop = EarlyStopping(monitor='val_loss',
min_delta=0.0001,
patience=3,
verbose=1,
mode='auto')
callbacks_list = [earlystop]
print model.summary()
model.fit([train_x, train_lda], [train_y],
batch_size=128,
epochs=100,
verbose=1,
shuffle=True,
callbacks=callbacks_list,
validation_data=[[val_x, val_lda], [val_y]])
#model.fit([train_x, train_lda], [train_y, train_lda], batch_size=64, epochs=25,
# verbose=1, shuffle=True)
test_predictions = model.predict([test_x, test_lda], verbose=False)
#test_predictions1k = model.predict([test_x1k, test_lda1k], verbose=False)
test_y = [np.argmax(pred) for pred in test_y]
test_pred = [np.argmax(pred) for pred in test_predictions]
#test_pred1k = [np.argmax(pred) for pred in test_predictions1k]
#print test_pred1k
#test_y = [np.argmax(label) for label in test_y]
#test_y1k = [np.argmax(label) for label in test_y1k]
error_preds = [
i for i in range(0, len(test_pred)) if (test_y[i] != test_pred[i])
]
print len(error_preds)
misclassified = [test_x[i] for i in error_preds]
misclassified = [[get_id2word(idx, idx2word) for idx in sent if idx != 0]
for sent in misclassified]
labels = [(test_y[i], test_pred[i]) for i in error_preds]
acc = accuracy_score(test_y, test_pred)
print acc
#acc1k = f1_score(test_y1k, test_pred1k, average='macro')
#print acc1k
return acc, misclassified, labels
x = Flatten()(x)
x = Dense(256, name='fc3')(x)
x = BatchNormalization()(x)
x = Activation('relu')(x)
x = Dense(64, name='fc4')(x)
x = BatchNormalization()(x)
x = Activation('relu')(x)
x = Dense(11, name='fc5')(x)
x = BatchNormalization()(x)
logit = Activation('softmax')(x)
netowrk = Model(input, logit)
print('netowrk build finish')
x = np.load('data/wv_mat3.npy')
y = np.load('data/onehotlable.npy')
print('data load finish')
opt = SGD(lr=0.1, momentum=0.7, decay=0.9)
netowrk.compile(loss='categorical_crossentropy',
optimizer='RMSprop',
metrics=['accuracy'])
netowrk.fit(x,
y,
batch_size=32,
if mode == 3:
train_X_ex = np.expand_dims(np.array(train_mfccs), -1)
test_X_ex = np.expand_dims(np.array(test_mfccs), -1)
print('train X shape:', train_X_ex.shape)
print('test X shape:', test_X_ex.shape)
ip = Input(shape=train_X_ex[0].shape)
m = Conv2D(64, kernel_size=(4, 4), activation='relu')(ip)
m = MaxPooling2D(pool_size=(4, 4))(m)
# m = Conv2D(128, kernel_size=(2, 2), activation='relu')(ip)
# m = MaxPooling2D(pool_size=(2, 2))(m)
m = Flatten()(m)
m = Dense(32, activation='relu')(m)
op = Dense(class_num, activation='softmax')(m)
model = Model(input=ip, output=op)
model.summary()
model.compile(
loss='categorical_crossentropy',
# maybe try using different optimizer
optimizer='adam',
metrics=['acc'])
history = model.fit(train_X_ex,
train_y,
epochs=epochs,
batch_size=32,
validation_data=(test_X_ex, test_y))
def run(_run, image_shape, data_dir, patches, estimator_type, submission_info,
solution, architecture, weights, batch_size, last_base_layer,
use_gram_matrix, pooling, dense_layers, device, chunks, limb_weights,
dropout_rate, ckpt, results_file, submission_file, use_multiprocessing,
workers, outputs_meta, limb_dense_layers, joint_weights):
report_dir = _run.observers[0].dir
with tf.device(device):
print('building...')
model = build_siamese_mo_model(image_shape,
architecture,
outputs_meta,
dropout_rate,
weights,
last_base_layer=last_base_layer,
use_gram_matrix=use_gram_matrix,
limb_dense_layers=limb_dense_layers,
pooling=pooling,
trainable_limbs=False,
limb_weights=limb_weights,
trainable_joints=False,
joint_weights=joint_weights,
dense_layers=dense_layers)
print('loading weights from', ckpt)
model.load_weights(ckpt)
x = []
for m in outputs_meta:
name = m['n']
shape = [m['e']]
x += [
Input(shape, name='%s_ia' % name),
Input(shape, name='%s_ib' % name)
]
o = []
for i, m in enumerate(outputs_meta):
name = m['n']
y = [x[2 * i], x[2 * i + 1]]
y = model.get_layer('multiply_%i' % (i + 1))(y)
y = model.get_layer('%s_binary_predictions' % name)(y)
o += [y]
rest = model.layers.index(model.get_layer('concatenate_asg'))
for l in model.layers[rest:]:
o = l(o)
meta_model = Model(inputs=x, outputs=o)
del model
print('loading submission and solution...')
pairs = pd.read_csv(submission_info, quotechar='"',
delimiter=',').values[:, 1:]
labels = pd.read_csv(solution, quotechar='"',
delimiter=',').values[:, 1:].flatten()
print('loading sequential predictions...')
d = load_pickle_data(data_dir,
phases=['test'],
keys=['data', 'names'],
chunks=chunks)
samples, names = d['test']
samples = np.asarray(
list(zip(*(samples['%s_em3' % o['n']] for o in outputs_meta))))
samples, names = group_by_paintings(samples, names=names)
names = np.asarray([n.split('/')[1] + '.jpg' for n in names])
print('test data shape:', samples.shape)
print('\n# test evaluation')
test_data = ArrayPairsSequence(samples, names, pairs, labels,
batch_size)
probabilities = meta_model.predict_generator(
test_data,
use_multiprocessing=use_multiprocessing,
workers=workers,
verbose=1).reshape(-1, patches)
del meta_model
K.clear_session()
layer_results = evaluate(labels, probabilities, estimator_type)
layer_results['phase'] = 'test'
evaluation_results = [layer_results]
# generate results file.
with open(os.path.join(report_dir, results_file), 'w') as file:
json.dump(evaluation_results, file)
# generate submission file to Kaggle.
for v in layer_results['evaluations']:
predictions_field = 'binary_probabilities' if 'binary_probabilities' in v else 'p'
p = v[predictions_field]
with open(
os.path.join(report_dir,
submission_file.format(strategy=v['strategy'])),
'w') as f:
f.write('index,sameArtist\n')
f.writelines(['%i,%f\n' % (i, _p) for i, _p in enumerate(p)])
def _init_translation_ranker(self,
l_field_translate,
ltr_input=None,
q_att_input=None,
l_field_att_input=None,
aux=False):
"""
construct ranker for given inputs
:param l_field_translate: translaiton matrices
:param ltr_input: if use ltr features to combine
:param q_att_input: q attention input
:param l_field_att_input: field attention input
:param aux:
:return:
"""
pre = ""
if aux:
pre = self.aux_pre
q_att = None
l_field_att = []
if self.with_attention:
if not aux:
self.l_q_att_in = q_att_input
self.l_field_att_in = l_field_att_input
q_att = Reshape(target_shape=(-1, 1, 1))(self.q_att(q_att_input))
l_field_att = [
Reshape(target_shape=(1, -1, 1))(self.l_field_att[p](
l_field_att_input[p]))
for p in xrange(len(self.l_field_att))
]
# perform kernel pooling
l_kp_features = []
for p in xrange(len(self.l_d_field)):
# field = self.l_d_field[p]
f_in = l_field_translate[p]
d_layer = self.kernel_pool(f_in)
# TODO test
if self.with_attention:
# need custom multiple layer to do * along target axes
# use broadcast reshape attention to targeted dimensions, and then use multiply
# q_att = Reshape(target_shape=(-1, 1, 1))(q_att)
d_layer = multiply([d_layer, q_att])
# l_field_att[p] = Reshape(target_shape=(1, -1, 1))(l_field_att[p])
d_layer = multiply([d_layer, l_field_att[p]])
if not aux:
self.l_d_layer.append(d_layer)
d_layer = self.kp_logsum(d_layer)
l_kp_features.append(d_layer)
# put features to one vector
if len(l_kp_features) > 1:
ranking_features = concatenate(l_kp_features,
name=pre + 'ranking_features')
else:
ranking_features = l_kp_features[0]
# # test
# test_model = Model(inputs=l_field_translate, outputs=ranking_features)
# test_model.summary()
if ltr_input:
ranking_features = concatenate([ranking_features, ltr_input],
name=pre +
'ranking_features_with_ltr')
ranking_layer = self.ltr_layer(ranking_features)
l_full_inputs = l_field_translate
if self.with_attention:
l_full_inputs.append(q_att_input)
l_full_inputs.extend(l_field_att_input)
if ltr_input:
l_full_inputs.append(ltr_input)
ranker = Model(inputs=l_full_inputs,
outputs=ranking_layer,
name=pre + 'ranker')
return ranker
print('Loading previously trained model1...')
model = load_model(previouslytrainedModelpath)
print(previouslytrainedModelpath + ' successfully loaded!')
custom_resnet_model=model
else :
print('Initializing resnet50 model1')
model = ResNet50(input_tensor=image_input, include_top=True,weights='imagenet')
model.summary()
# sys.exit(1)
x = model.get_layer('res5a_branch2a').input
x = GlobalAveragePooling2D(name='avg_pool')(x)
# x = Dense(512, activation='relu',name='fc-1')(x)
x = Dropout(0.5)(x)
out = Dense(num_classes, activation='softmax', name='output_layer')(x)
custom_resnet_model = Model(inputs=image_input,outputs= out)
#custom_resnet_model.summary()
for layer in custom_resnet_model.layers[:]:
layer.trainable = True
#custom_resnet_model.layers[-1].trainable
#custom_resnet_model.compile(loss='categorical_crossentropy',optimizer='adam',metrics=['accuracy'])
# compile the model with a SGD/momentum optimizer
# and a very slow learning rate.
custom_resnet_model.compile(loss='categorical_crossentropy',
optimizer=optimizers.SGD(lr=learningrate, momentum=momentum),
def train_rpn(model_file=None):
parser = OptionParser()
parser.add_option("--train_path", dest="train_path", help="Path to training data.",
default='/Users/jie/projects/PanelSeg/ExpPython/train.txt')
parser.add_option("--val_path", dest="val_path", help="Path to validation data.",
default='/Users/jie/projects/PanelSeg/ExpPython/eval.txt')
parser.add_option("--num_rois", type="int", dest="num_rois", help="Number of RoIs to process at once.",
default=32)
parser.add_option("--network", dest="network", help="Base network to use. Supports nn_cnn_3_layer.",
default='nn_cnn_3_layer')
parser.add_option("--num_epochs", type="int", dest="num_epochs", help="Number of epochs.",
default=2000)
parser.add_option("--output_weight_path", dest="output_weight_path", help="Output path for weights.",
default='./model_rpn.hdf5')
parser.add_option("--input_weight_path", dest="input_weight_path",
default='/Users/jie/projects/PanelSeg/ExpPython/models/label+bg_rpn_3_layer_color-0.135.hdf5')
(options, args) = parser.parse_args()
# set configuration
c = Config.Config()
c.model_path = options.output_weight_path
c.num_rois = int(options.num_rois)
import nn_cnn_3_layer as nn
c.base_net_weights = options.input_weight_path
val_imgs, val_classes_count = get_label_rpn_data(options.val_path)
train_imgs, train_classes_count = get_label_rpn_data(options.train_path)
classes_count = {k: train_classes_count.get(k, 0) + val_classes_count.get(k, 0)
for k in set(train_classes_count) | set(val_classes_count)}
class_mapping = LABEL_MAPPING
if 'bg' not in classes_count:
classes_count['bg'] = 0
class_mapping['bg'] = len(class_mapping)
c.class_mapping = class_mapping
inv_map = {v: k for k, v in class_mapping.items()}
print('Training images per class:')
pprint.pprint(classes_count)
print('Num classes (including bg) = {}'.format(len(classes_count)))
config_output_filename = 'config.pickle'
with open(config_output_filename, 'wb') as config_f:
pickle.dump(c, config_f)
print('Config has been written to {}, and can be loaded when testing to ensure correct results'.format(
config_output_filename))
random.shuffle(train_imgs)
random.shuffle(val_imgs)
num_imgs = len(train_imgs) + len(val_imgs)
print('Num train samples {}'.format(len(train_imgs)))
print('Num val samples {}'.format(len(val_imgs)))
data_gen_train = label_rcnn_data_generators.get_anchor_gt(
train_imgs, classes_count, c, nn.nn_get_img_output_length, mode='train')
data_gen_val = label_rcnn_data_generators.get_anchor_gt(
val_imgs, classes_count, c, nn.nn_get_img_output_length, mode='val')
input_shape_img = (None, None, 3)
img_input = Input(shape=input_shape_img)
# roi_input = Input(shape=(None, 4))
# define the base network (resnet here, can be VGG, Inception, etc)
shared_layers = nn.nn_base(img_input, trainable=True)
# define the RPN, built on the base layers
num_anchors = len(c.anchor_box_scales) * len(c.anchor_box_ratios)
rpn = nn.rpn(shared_layers, num_anchors)
# classifier = nn.classifier(shared_layers, roi_input, c.num_rois, nb_classes=len(classes_count), trainable=True)
model_rpn = Model(img_input, rpn[:2])
# model_classifier = Model([img_input, roi_input], classifier)
# this is a model that holds both the RPN and the classifier, used to load/save weights for the models
# model_all = Model([img_input, roi_input], rpn[:2] + classifier)
print('loading weights from {}'.format(c.base_net_weights))
model_rpn.load_weights(c.base_net_weights, by_name=True)
# model_classifier.load_weights(c.base_net_weights, by_name=True)
model_rpn.summary()
optimizer = Adam(lr=1e-5)
# optimizer_classifier = Adam(lr=1e-5)
model_rpn.compile(optimizer=optimizer, loss=[nn.rpn_loss_cls(num_anchors), nn.rpn_loss_regr(num_anchors)])
# model_classifier.compile(optimizer=optimizer_classifier,
# loss=[nn.class_loss_cls, nn.class_loss_regr(len(classes_count) - 1)],
# metrics={'dense_class_{}'.format(len(classes_count)): 'accuracy'})
# model_all.compile(optimizer='sgd', loss='mae')
epoch_length = 1000
num_epochs = int(options.num_epochs)
iter_num = 0
losses = np.zeros((epoch_length, 5))
rpn_accuracy_rpn_monitor = []
rpn_accuracy_for_epoch = []
start_time = time.time()
best_loss = np.Inf
class_mapping_inv = {v: k for k, v in class_mapping.items()}
print('Starting training')
vis = True
for epoch_num in range(num_epochs):
progbar = generic_utils.Progbar(epoch_length)
print('Epoch {}/{}'.format(epoch_num + 1, num_epochs))
while True:
try:
if len(rpn_accuracy_rpn_monitor) == epoch_length and c.verbose:
mean_overlapping_bboxes = float(sum(rpn_accuracy_rpn_monitor)) / len(rpn_accuracy_rpn_monitor)
rpn_accuracy_rpn_monitor = []
print('Average number of overlapping bounding boxes from RPN = {} for {} previous iterations'.format(
mean_overlapping_bboxes, epoch_length))
if mean_overlapping_bboxes == 0:
print('RPN is not producing bounding boxes that overlap the ground truth boxes. Check RPN settings or keep training.')
X, Y, img_data = next(data_gen_train)
loss_rpn = model_rpn.train_on_batch(X, Y)
P_rpn = model_rpn.predict_on_batch(X)
R = label_rcnn_roi_helpers.rpn_to_roi(P_rpn[0], P_rpn[1], c, K.image_dim_ordering(), use_regr=True,
overlap_thresh=0.7, max_boxes=300)
# note: calc_iou converts from (x1,y1,x2,y2) to (x,y,w,h) format
X2, Y1, Y2, IouS = label_rcnn_roi_helpers.calc_iou(R, img_data, c, class_mapping)
if X2 is None:
rpn_accuracy_rpn_monitor.append(0)
rpn_accuracy_for_epoch.append(0)
continue
neg_samples = np.where(Y1[0, :, -1] == 1)
pos_samples = np.where(Y1[0, :, -1] == 0)
if len(neg_samples) > 0:
neg_samples = neg_samples[0]
else:
neg_samples = []
if len(pos_samples) > 0:
pos_samples = pos_samples[0]
else:
pos_samples = []
rpn_accuracy_rpn_monitor.append(len(pos_samples))
rpn_accuracy_for_epoch.append((len(pos_samples)))
if c.num_rois > 1:
if len(pos_samples) < c.num_rois // 2:
selected_pos_samples = pos_samples.tolist()
else:
selected_pos_samples = np.random.choice(pos_samples, c.num_rois // 2, replace=False).tolist()
try:
selected_neg_samples = np.random.choice(neg_samples, c.num_rois - len(selected_pos_samples),
replace=False).tolist()
except:
selected_neg_samples = np.random.choice(neg_samples, c.num_rois - len(selected_pos_samples),
replace=True).tolist()
sel_samples = selected_pos_samples + selected_neg_samples
else:
# in the extreme case where num_rois = 1, we pick a random pos or neg sample
selected_pos_samples = pos_samples.tolist()
selected_neg_samples = neg_samples.tolist()
if np.random.randint(0, 2):
sel_samples = random.choice(neg_samples)
else:
sel_samples = random.choice(pos_samples)
# loss_class = model_classifier.train_on_batch([X, X2[:, sel_samples, :]],
# [Y1[:, sel_samples, :], Y2[:, sel_samples, :]])
losses[iter_num, 0] = loss_rpn[1]
losses[iter_num, 1] = loss_rpn[2]
# losses[iter_num, 2] = loss_class[1]
# losses[iter_num, 3] = loss_class[2]
# losses[iter_num, 4] = loss_class[3]
iter_num += 1
progbar.update(iter_num,
[('rpn_cls', np.mean(losses[:iter_num, 0])),
('rpn_regr', np.mean(losses[:iter_num, 1]))])
# progbar.update(iter_num,
# [('rpn_cls', np.mean(losses[:iter_num, 0])),
# ('rpn_regr', np.mean(losses[:iter_num, 1])),
# ('detector_cls', np.mean(losses[:iter_num, 2])),
# ('detector_regr', np.mean(losses[:iter_num, 3]))])
if iter_num == epoch_length:
loss_rpn_cls = np.mean(losses[:, 0])
loss_rpn_regr = np.mean(losses[:, 1])
# loss_class_cls = np.mean(losses[:, 2])
# loss_class_regr = np.mean(losses[:, 3])
# class_acc = np.mean(losses[:, 4])
mean_overlapping_bboxes = float(sum(rpn_accuracy_for_epoch)) / len(rpn_accuracy_for_epoch)
rpn_accuracy_for_epoch = []
if c.verbose:
print('Mean number of bounding boxes from RPN overlapping ground truth boxes: {}'.format(
mean_overlapping_bboxes))
# print('Classifier accuracy for bounding boxes from RPN: {}'.format(class_acc))
print('Loss RPN classifier: {}'.format(loss_rpn_cls))
print('Loss RPN regression: {}'.format(loss_rpn_regr))
# print('Loss Detector classifier: {}'.format(loss_class_cls))
# print('Loss Detector regression: {}'.format(loss_class_regr))
print('Elapsed time: {}'.format(time.time() - start_time))
curr_loss = loss_rpn_cls + loss_rpn_regr
# curr_loss = loss_rpn_cls + loss_rpn_regr + loss_class_cls + loss_class_regr
iter_num = 0
start_time = time.time()
if curr_loss < best_loss:
if c.verbose:
print('Total loss decreased from {} to {}, saving weights'.format(best_loss, curr_loss))
best_loss = curr_loss
model_rpn.save_weights(c.model_path)
# model_all.save_weights(c.model_path)
break
except Exception as e:
print('Exception: {}'.format(e))
continue
print('Training complete, exiting.')
def unet_model_3d(input_shape,
pool_size=(2, 2, 2),
n_labels=1,
initial_learning_rate=0.00001,
deconvolution=False,
depth=4,
n_base_filters=32,
include_label_wise_dice_coefficients=False,
metrics=dice_coefficient,
batch_normalization=True,
activation_name="sigmoid"):
inputs = Input(input_shape)
current_layer = inputs
levels = list()
# add levels with max pooling
for layer_depth in range(depth):
layer1 = create_convolution_block(
input_layer=current_layer,
n_filters=n_base_filters * (2**layer_depth),
batch_normalization=batch_normalization)
layer2 = create_convolution_block(
input_layer=layer1,
n_filters=n_base_filters * (2**layer_depth) * 2,
batch_normalization=batch_normalization)
if layer_depth < depth - 1:
current_layer = MaxPooling3D(pool_size=pool_size)(layer2)
levels.append([layer1, layer2, current_layer])
else:
current_layer = layer2
levels.append([layer1, layer2])
# add levels with up-convolution or up-sampling
for layer_depth in range(depth - 2, -1, -1):
up_convolution = get_up_convolution(
pool_size=pool_size,
deconvolution=deconvolution,
n_filters=current_layer._keras_shape[1])(current_layer)
concat = concatenate([up_convolution, levels[layer_depth][1]], axis=4)
current_layer = create_convolution_block(
n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=concat,
batch_normalization=batch_normalization)
current_layer = create_convolution_block(
n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=current_layer,
batch_normalization=batch_normalization)
final_convolution = Conv3D(n_labels, (1, 1, 1))(current_layer)
act = Activation(activation_name)(final_convolution)
model = Model(inputs=inputs, outputs=act)
if not isinstance(metrics, list):
metrics = [metrics]
if include_label_wise_dice_coefficients and n_labels > 1:
label_wise_dice_metrics = [
get_label_dice_coefficient_function(index)
for index in range(n_labels)
]
if metrics:
metrics = metrics + label_wise_dice_metrics
else:
metrics = label_wise_dice_metrics
model.compile(optimizer=Adam(lr=initial_learning_rate),
loss=dice_coefficient_loss,
metrics=metrics)
return model
def build_model(self):
input_tensor = Input(batch_shape=self.input_shape)
last_layer_name = 'activation_22'
base_model = ResNet50(include_top=False,
input_tensor=input_tensor,
weights=None)
base_model_out = base_model.get_layer(last_layer_name).output
model = Model(input=base_model.input, output=base_model_out)
no_features = base_model_out.get_shape()[3].value
model = Convolution2D(no_features,
1,
1,
border_mode='same',
activation='relu')(model.output)
model = Dropout(0.5)(model)
class_out = Deconvolution2D(self.out_channels,
8,
8,
output_shape=self.output_shape,
subsample=(8, 8),
activation='sigmoid',
name='class_out')(model)
model = Model(base_model.input, output=class_out)
optimizer = Adam(lr=self.learning_rate,
beta_1=0.9,
beta_2=0.999,
epsilon=1e-08,
decay=0.0)
model.compile(optimizer=optimizer,
loss={'class_out': 'binary_crossentropy'},
metrics=['binary_accuracy'])
for i, layer in enumerate(model.layers):
layer.trainable = False
if layer.name == last_layer_name:
break
if self.weight_file:
logger.info('Loading weights from :{}', self.weight_file)
model.load_weights(self.weight_file)
logger.info('Compiled fully conv with output:{}', model.output)
model.summary()
return model
def unet_model_3d(input_shape,
downsize_filters_factor=1,
pool_size=(2, 2, 2),
n_labels=1,
initial_learning_rate=0.01,
deconvolution=False):
"""
Builds the 3D U-Net Keras model.
The [U-Net](https://arxiv.org/abs/1505.04597) uses a fully-convolutional architecture consisting of an
encoder and a decoder. The encoder is able to capture contextual information while the decoder enables
precise localization. Due to the large amount of parameters, the input shape has to be small since for e.g.
images of shape 144x144x144 the model already consumes 32 GB of memory.
:param input_shape: Shape of the input data (x_size, y_size, z_size, n_channels).
:param downsize_filters_factor: Factor to which to reduce the number of filters. Making this value larger
will reduce the amount of memory the model will need during training.
:param pool_size: Pool size for the max pooling operations.
:param n_labels: Number of binary labels that the model is learning.
:param initial_learning_rate: Initial learning rate for the model. This will be decayed during training.
:param deconvolution: If set to True, will use transpose convolution(deconvolution) instead of upsamping.
This increases the amount memory required during training.
:return: Untrained 3D UNet Model
"""
inputs = Input(input_shape)
conv1 = Conv3D(int(32 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(inputs)
conv1 = Conv3D(int(64 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv1)
pool1 = MaxPooling3D(pool_size=pool_size)(conv1)
conv2 = Conv3D(int(64 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(pool1)
conv2 = Conv3D(int(128 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv2)
pool2 = MaxPooling3D(pool_size=pool_size)(conv2)
conv3 = Conv3D(int(128 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(pool2)
conv3 = Conv3D(int(256 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv3)
print(conv3.shape)
pool3 = MaxPooling3D(pool_size=pool_size)(conv3)
conv4 = Conv3D(int(256 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(pool3)
conv4 = Conv3D(int(512 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv4)
print(conv4.shape)
up5 = get_upconv(pool_size=pool_size,
deconvolution=deconvolution,
depth=2,
nb_filters=int(512 / downsize_filters_factor),
image_shape=input_shape[-3:])(conv4)
print(up5.shape)
up5 = concatenate([up5, conv3], axis=4)
conv5 = Conv3D(int(256 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(up5)
conv5 = Conv3D(int(256 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv5)
up6 = get_upconv(pool_size=pool_size,
deconvolution=deconvolution,
depth=1,
nb_filters=int(256 / downsize_filters_factor),
image_shape=input_shape[-3:])(conv5)
up6 = concatenate([up6, conv2], axis=4)
conv6 = Conv3D(int(128 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(up6)
conv6 = Conv3D(int(128 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv6)
up7 = get_upconv(pool_size=pool_size,
deconvolution=deconvolution,
depth=0,
nb_filters=int(128 / downsize_filters_factor),
image_shape=input_shape[-3:])(conv6)
up7 = concatenate([up7, conv1], axis=4)
conv7 = Conv3D(int(64 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(up7)
conv7 = Conv3D(int(64 / downsize_filters_factor), (3, 3, 3),
activation='relu',
padding='same')(conv7)
conv8 = Conv3D(n_labels, (1, 1, 1))(conv7)
act = Activation('sigmoid')(conv8)
model = Model(inputs=inputs, outputs=act)
model.compile(optimizer=Adam(lr=initial_learning_rate),
loss=SegmentationModel.dice_coef_loss,
metrics=[SegmentationModel.dice_coef])
return model
def unormalise(x):
# outputs in range [0, 1] resized to range [-100, 100]
return (x * 200) - 100
last = Lambda(resize_image)(last)
last = Lambda(unormalise)(last)
def custom_mse(y_true, y_pred):
return K.mean(K.square(y_pred - y_true), axis=[1, 2, 3])
model = Model(inputs=[main_input, vgg16.input], output=last)
opt = optimizers.Adam(lr=1E-4, beta_1=0.9, beta_2=0.999, epsilon=1e-08)
model.compile(optimizer=opt, loss=custom_mse)
model.summary()
start_from = 160
save_every_n_epoch = 10
n_epochs = 300
model.load_weights("../weights/implementation7l-150.h5")
g = image_processing.image_generator_parts(list_dir,
b_size,
im_size=(224, 224))
def run(dataset_seed, image_shape, batch_size, device, data_dir, output_dir,
phases, architecture, include_base_top, include_top, o_meta, ckpt_file,
weights, pooling, dense_layers, use_gram_matrix, last_base_layer,
override, embedded_files_max_size, selected_layers):
os.makedirs(output_dir, exist_ok=True)
with tf.device(device):
print('building model...')
model = build_model(image_shape,
architecture=architecture,
weights=weights,
dropout_p=.0,
pooling=pooling,
last_base_layer=last_base_layer,
use_gram_matrix=use_gram_matrix,
dense_layers=dense_layers,
include_base_top=include_base_top,
include_top=include_top,
classes=[o['u'] for o in o_meta],
predictions_name=[o['n'] for o in o_meta],
predictions_activation=[o['a'] for o in o_meta])
if ckpt_file:
# Restore best parameters.
print('loading weights from:', ckpt_file)
model.load_weights(ckpt_file)
available_layers = [l.name for l in model.layers]
if set(selected_layers) - set(available_layers):
print('available layers:', available_layers)
raise ValueError('selection contains unknown layers: %s' %
selected_layers)
style_features = [model.get_layer(l).output for l in selected_layers]
if use_gram_matrix:
gram_layer = layers.Lambda(gram_matrix,
arguments=dict(norm_by_channels=False))
style_features = [gram_layer(f) for f in style_features]
model = Model(inputs=model.inputs, outputs=style_features)
g = ImageDataGenerator(
preprocessing_function=get_preprocess_fn(architecture))
for phase in phases:
phase_data_dir = os.path.join(data_dir, phase)
output_file_name = os.path.join(output_dir, phase + '.%i.pickle')
already_embedded = os.path.exists(output_file_name % 0)
phase_exists = os.path.exists(phase_data_dir)
if already_embedded and not override or not phase_exists:
print('%s transformation skipped' % phase)
continue
# Shuffle must always be off in order to keep names consistent.
data = g.flow_from_directory(phase_data_dir,
target_size=image_shape[:2],
class_mode='sparse',
batch_size=batch_size,
shuffle=False,
seed=dataset_seed)
print('transforming %i %s samples from %s' %
(data.n, phase, phase_data_dir))
part_id = 0
samples_seen = 0
displayed_once = False
while samples_seen < data.n:
z, y = {n: [] for n in selected_layers}, []
chunk_size = 0
chunk_start = samples_seen
while chunk_size < embedded_files_max_size and samples_seen < data.n:
_x, _y = next(data)
outputs = model.predict_on_batch(_x)
if not isinstance(outputs, list):
outputs = [outputs]
chunk_size += sum(o.nbytes for o in outputs)
for l, o in zip(selected_layers, outputs):
z[l].append(o)
y.append(_y)
samples_seen += _x.shape[0]
chunk_p = int(100 * (samples_seen / data.n))
if chunk_p % 10 == 0:
if not displayed_once:
print('\n%i%% (shape=%s, size=%.2f MB)' %
(chunk_p, _x.shape, chunk_size / 1024**2),
flush=True,
end='')
displayed_once = True
else:
displayed_once = False
print('.', end='')
for layer in selected_layers:
z[layer] = np.concatenate(z[layer])
with open(output_file_name % part_id, 'wb') as f:
pickle.dump(
{
'data':
z,
'target':
np.concatenate(y),
'names':
np.asarray(data.filenames[chunk_start:samples_seen])
}, f, pickle.HIGHEST_PROTOCOL)
part_id += 1
print('done.')
def complex_model2(input_length, output_levels, stride, receptive_field, nb_filters_, loading=False, path=""):
fnn_init = 'he_uniform'
def residual_block(input_):
original = input_
tanh_ = AtrousConvolution1D(
nb_filter=nb_filters_,
filter_length=2,
atrous_rate=2**i,
init=fnn_init,
border_mode='valid',
bias=False,
causal=True,
activation='tanh',
name='AtrousConv1D_%d_tanh' % (2**i)
)(input_)
sigmoid_ = AtrousConvolution1D(
nb_filter=nb_filters_,
filter_length=2,
atrous_rate=2**i,
init=fnn_init,
border_mode='valid',
bias=False,
causal=True,
activation='sigmoid',
name='AtrousConv1D_%d_sigm' % (2**i)
)(input_)
input_ = Merge(mode='mul')([tanh_, sigmoid_])
res_x = Convolution1D(nb_filter=nb_filters_, filter_length=1, border_mode='same', bias=False)(input_)
skip_c = res_x
res_x = Merge(mode='sum')([original, res_x])
return res_x, skip_c
input = Input(shape=(input_length, output_levels), name='input_part')
skip_connections = []
output = input
output = AtrousConvolution1D(
nb_filter=nb_filters_,
filter_length=2,
atrous_rate=1,
init=fnn_init,
activation='relu',
border_mode='valid',
causal=True,
name='initial_AtrousConv1D'
)(output)
for i in range( int(np.log2( receptive_field ) ) ):
output, skip_c = residual_block(output)
skip_connections.append(skip_c)
out = Merge(mode='sum')(skip_connections)
for _ in range(2):
out = Activation('relu')(out)
out = Convolution1D(output_levels, 1, activation=None, border_mode='same')(out)
out = Activation('softmax', name='output_softmax')(out)
#out = Reshape((dim1, nb_filters_*dim2))(out)
output = TimeDistributed(Dense(output_dim=output_levels, init=fnn_init, activation='softmax'))(out)
m = Model(input, output)
if loading:
m.load_weights(path)
print "Weights loaded!"
#ADAM = Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-05, decay=0.0)
m.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
return m
similar_persons,
similar_matrix,
train=True,
source_datas=class_img_labels),
triplet_generator_by_rank_list(train_images,
batch_size,
similar_persons,
similar_matrix,
train=False,
source_datas=class_img_labels),
source_pair_model_path,
target_model_path,
batch_size=batch_size)
if __name__ == '__main__':
pair_model = load_model('../pretrain/cuhk_pair_pretrain.h5')
# pair_model = load_model('../cuhk_market-rank_transfer.h5')
base_model = pair_model.layers[3]
base_model = Model(inputs=base_model.get_input_at(0),
outputs=[base_model.get_output_at(0)],
name='resnet50')
print isinstance(base_model.layers[-20], Conv2D)
print isinstance(base_model.layers[-20], BatchNormalization)
rank_transfer_2dataset(
'../pretrain/cuhk_pair_pretrain.h5', '../dataset/market_train.list',
'rank_transfer_test.h5', '/home/cwh/coding/Market-1501/train',
'/home/cwh/coding/rank-reid/data_clean/cross_filter_pid.log',
'/home/cwh/coding/rank-reid/data_clean/cross_filter_score.log')
def test_rpn():
parser = OptionParser()
parser.add_option("-p", "--path", dest="test_path", help="Path to test data.",
default='/Users/jie/projects/PanelSeg/ExpRcnn/eval.txt')
parser.add_option("-n", "--num_rois", type="int", dest="num_rois",
help="Number of ROIs per iteration. Higher means more memory use.", default=32)
parser.add_option("--config_filename", dest="config_filename",
help="Location to read the metadata related to the training (generated when training).",
default="config.pickle")
parser.add_option("--network", dest="network", help="Base network to use. Supports nn_cnn_3_layer.",
default='nn_cnn_3_layer')
parser.add_option("--rpn_weight_path", dest="rpn_weight_path",
default='/Users/jie/projects/PanelSeg/ExpRcnn/models/model_rpn_3_layer_color-0.0577.hdf5')
parser.add_option("--classify_model_path", dest="classify_model_path",
default='/Users/jie/projects/PanelSeg/ExpRcnn/models/label50+bg_cnn_3_layer_color-0.9910.h5')
(options, args) = parser.parse_args()
if not options.test_path: # if filename is not given
parser.error('Error: path to test data must be specified. Pass --path to command line')
config_output_filename = options.config_filename
with open(config_output_filename, 'rb') as f_in:
c = pickle.load(f_in)
import nn_cnn_3_layer as nn
# turn off any data augmentation at test time
c.use_horizontal_flips = False
c.use_vertical_flips = False
c.rot_90 = False
img_list_path = options.test_path
def format_img_size(img, C):
""" formats the image size based on config """
img_min_side = float(C.im_size)
(height, width, _) = img.shape
if width <= height:
ratio = img_min_side / width
new_height = int(ratio * height)
new_width = int(img_min_side)
else:
ratio = img_min_side / height
new_width = int(ratio * width)
new_height = int(img_min_side)
img = cv2.resize(img, (new_width, new_height), interpolation=cv2.INTER_CUBIC)
return img, ratio
def format_img_channels(img, C):
""" formats the image channels based on config """
# img = img[:, :, (2, 1, 0)]
img = img.astype(np.float32)
img[:, :, 0] -= C.img_channel_mean[0]
img[:, :, 1] -= C.img_channel_mean[1]
img[:, :, 2] -= C.img_channel_mean[2]
img /= 255
# img /= C.img_scaling_factor
img = np.transpose(img, (2, 0, 1))
img = np.expand_dims(img, axis=0)
return img
def format_img(img, C):
""" formats an image for model prediction based on config """
# img, ratio = format_img_size(img, C)
img = format_img_channels(img, C)
return img, 1.0
# Method to transform the coordinates of the bounding box to its original size
def get_real_coordinates(ratio, x1, y1, x2, y2):
real_x1 = int(round(x1 // ratio))
real_y1 = int(round(y1 // ratio))
real_x2 = int(round(x2 // ratio))
real_y2 = int(round(y2 // ratio))
return (real_x1, real_y1, real_x2, real_y2)
class_mapping = c.class_mapping
if 'bg' not in class_mapping:
class_mapping['bg'] = len(class_mapping)
class_mapping = {v: k for k, v in class_mapping.items()}
print(class_mapping)
class_to_color = {class_mapping[v]: np.random.randint(0, 255, 3) for v in class_mapping}
c.num_rois = int(options.num_rois)
# if c.network == 'resnet50':
# num_features = 1024
# elif c.network == 'vgg':
# num_features = 512
input_shape_img = (None, None, 3)
# input_shape_features = (None, None, num_features)
img_input = Input(shape=input_shape_img)
roi_input = Input(shape=(c.num_rois, 4))
# feature_map_input = Input(shape=input_shape_features)
# define the base network
shared_layers = nn.nn_base(img_input, trainable=True)
# define the RPN, built on the base layers
num_anchors = len(c.anchor_box_scales) * len(c.anchor_box_ratios)
rpn_layers = nn.rpn(shared_layers, num_anchors)
# classifier = nn.classifier(feature_map_input, roi_input, c.num_rois, nb_classes=len(class_mapping), trainable=True)
model_rpn = Model(img_input, rpn_layers)
# model_classifier_only = Model([feature_map_input, roi_input], classifier)
# model_classifier = Model([feature_map_input, roi_input], classifier)
print('Loading weights from {}'.format(c.model_path))
model_rpn.load_weights(options.rpn_weight_path, by_name=True)
# model_classifier.load_weights(c.model_path, by_name=True)
model_rpn.compile(optimizer='sgd', loss='mse')
# model_classifier.compile(optimizer='sgd', loss='mse')
model_rpn.summary()
model_classifier = load_model(options.classify_model_path)
model_classifier.summary()
all_imgs = []
classes = {}
bbox_threshold = 0.8
visualise = True
with open(img_list_path) as f:
lines = f.readlines()
for idx, filepath in enumerate(lines):
print(filepath)
st = time.time()
filepath = filepath.strip()
figure = Figure(filepath)
figure.load_image()
img = figure.image
X, ratio = format_img(img, c)
if K.image_dim_ordering() == 'tf':
X = np.transpose(X, (0, 2, 3, 1))
# get the feature maps and output from the RPN
[Y1, Y2, F] = model_rpn.predict(X)
R = label_rcnn_roi_helpers.rpn_to_roi(Y1, Y2, c, K.image_dim_ordering(), overlap_thresh=0.7)
# convert from (x1,y1,x2,y2) to (x,y,w,h)
R[:, 2] -= R[:, 0]
R[:, 3] -= R[:, 1]
patches = np.empty([R.shape[0], 28, 28, 3], dtype=int)
for idx, roi in enumerate(R):
x, y, w, h = roi[0], roi[1], roi[2], roi[3]
patch = figure.image[y:y + h, x:x + w]
patches[idx] = cv2.resize(patch, (28, 28))
patches = patches.astype('float32')
patches[:, :, :, 0] -= c.img_channel_mean[0]
patches[:, :, :, 1] -= c.img_channel_mean[1]
patches[:, :, :, 2] -= c.img_channel_mean[2]
patches /= 255
prediction = model_classifier.predict(patches)
# # apply the spatial pyramid pooling to the proposed regions
# bboxes = {}
# probs = {}
#
# for jk in range(R.shape[0] // c.num_rois + 1):
# ROIs = np.expand_dims(R[c.num_rois * jk:c.num_rois * (jk + 1), :], axis=0)
# if ROIs.shape[1] == 0:
# break
#
# if jk == R.shape[0] // c.num_rois:
# # pad R
# curr_shape = ROIs.shape
# target_shape = (curr_shape[0], c.num_rois, curr_shape[2])
# ROIs_padded = np.zeros(target_shape).astype(ROIs.dtype)
# ROIs_padded[:, :curr_shape[1], :] = ROIs
# ROIs_padded[0, curr_shape[1]:, :] = ROIs[0, 0, :]
# ROIs = ROIs_padded
#
# # [P_cls, P_regr] = model_classifier_only.predict([F, ROIs])
#
# for ii in range(P_cls.shape[1]):
#
# if np.max(P_cls[0, ii, :]) < bbox_threshold or np.argmax(P_cls[0, ii, :]) == (P_cls.shape[2] - 1):
# continue
#
# cls_name = class_mapping[np.argmax(P_cls[0, ii, :])]
#
# if cls_name not in bboxes:
# bboxes[cls_name] = []
# probs[cls_name] = []
#
# (x, y, w, h) = ROIs[0, ii, :]
#
# cls_num = np.argmax(P_cls[0, ii, :])
# try:
# (tx, ty, tw, th) = P_regr[0, ii, 4 * cls_num:4 * (cls_num + 1)]
# tx /= c.classifier_regr_std[0]
# ty /= c.classifier_regr_std[1]
# tw /= c.classifier_regr_std[2]
# th /= c.classifier_regr_std[3]
# x, y, w, h = label_rcnn_roi_helpers.apply_regr(x, y, w, h, tx, ty, tw, th)
# except:
# pass
# bboxes[cls_name].append(
# [c.rpn_stride * x, c.rpn_stride * y, c.rpn_stride * (x + w), c.rpn_stride * (y + h)])
# probs[cls_name].append(np.max(P_cls[0, ii, :]))
#
# all_dets = []
# for key in bboxes:
# bbox = np.array(bboxes[key])
#
# new_boxes, new_probs = label_rcnn_roi_helpers.non_max_suppression_fast(bbox, np.array(probs[key]), overlap_thresh=0.5)
# for jk in range(new_boxes.shape[0]):
# (x1, y1, x2, y2) = new_boxes[jk, :]
#
# (real_x1, real_y1, real_x2, real_y2) = get_real_coordinates(ratio, x1, y1, x2, y2)
#
# cv2.rectangle(img, (real_x1, real_y1), (real_x2, real_y2),
# (int(class_to_color[key][0]), int(class_to_color[key][1]), int(class_to_color[key][2])),
# 2)
#
# textLabel = '{}: {}'.format(key, int(100 * new_probs[jk]))
# all_dets.append((key, 100 * new_probs[jk]))
#
# (retval, baseLine) = cv2.getTextSize(textLabel, cv2.FONT_HERSHEY_COMPLEX, 1, 1)
# textOrg = (real_x1, real_y1 - 0)
#
# cv2.rectangle(img, (textOrg[0] - 5, textOrg[1] + baseLine - 5),
# (textOrg[0] + retval[0] + 5, textOrg[1] - retval[1] - 5), (0, 0, 0), 2)
# cv2.rectangle(img, (textOrg[0] - 5, textOrg[1] + baseLine - 5),
# (textOrg[0] + retval[0] + 5, textOrg[1] - retval[1] - 5), (255, 255, 255), -1)
# cv2.putText(img, textLabel, textOrg, cv2.FONT_HERSHEY_DUPLEX, 1, (0, 0, 0), 1)
print('Elapsed time = {}'.format(time.time() - st))
# print(all_dets)
cv2.imshow('img', img)
cv2.waitKey(0)
def train_pair_predict(pair_model_path, target_train_path, pid_path, score_path):
model = load_model(pair_model_path)
model = Model(inputs=[model.get_layer('resnet50').get_input_at(0)],
outputs=[model.get_layer('resnet50').get_output_at(0)])
train_predict(model, target_train_path, pid_path, score_path)
def train_label_none_label_classification(label_folder, non_label_folder, model_file=None):
c = Config()
# Build or load model
if model_file is None:
# create model
img_input = Input(shape=(28, 28, 3))
# prediction = model_cnn_2_layer.nn_classify_label_non_label(img_input)
# prediction = model_cnn_3_layer.nn_classify_label_non_label(img_input)
prediction = nn_cnn_3_layer.nn_classify_label_non_label(img_input)
model = Model(inputs=img_input, outputs=prediction)
model.compile(loss='categorical_crossentropy', optimizer=RMSprop(), metrics=['accuracy'])
else:
model = load_model(model_file)
model.summary()
# Load and normalize data
x_train, y_train, x_test, y_test = load_train_validation_data(label_folder, non_label_folder)
x_train = x_train.astype('float32')
x_test = x_test.astype('float32')
x_train[:, :, :, 0] -= c.img_channel_mean[0]
x_train[:, :, :, 1] -= c.img_channel_mean[1]
x_train[:, :, :, 2] -= c.img_channel_mean[2]
x_test[:, :, :, 0] -= c.img_channel_mean[0]
x_test[:, :, :, 1] -= c.img_channel_mean[1]
x_test[:, :, :, 2] -= c.img_channel_mean[2]
x_train /= 255
x_test /= 255
print(x_train.shape[0], 'train samples')
print(x_test.shape[0], 'test samples')
# x_train.reshape(x_train.shape[0], 28, 28, 3)
# x_test.reshape(x_test.shape[0], 28, 28, 3)
# convert class vectors to binary class matrices
y_train = keras.utils.to_categorical(y_train, 2)
y_test = keras.utils.to_categorical(y_test, 2)
# Checkpointing is to save the network weights only when there is an improvement in classification accuracy
# on the validation dataset (monitor=’val_acc’ and mode=’max’).
file_path = "weights-improvement-{epoch:04d}-{val_acc:.4f}.hdf5"
checkpoint = ModelCheckpoint(file_path, monitor='val_acc', verbose=1, save_best_only=True, mode='max')
callbacks_list = [checkpoint]
model.fit(x_train, y_train,
batch_size=128,
epochs=100,
verbose=1,
callbacks=callbacks_list,
validation_data=(x_test, y_test)
)
score = model.evaluate(x_test, y_test, verbose=0)
print('Test loss:', score[0])
print('Test accuracy:', score[1])
model.save('final_model.h5')
def train_rank_predict(rank_model_path, target_train_path, pid_path, score_path):
model = load_model(rank_model_path, custom_objects={'cross_entropy_loss': cross_entropy_loss})
model = Model(inputs=[model.get_layer('resnet50').get_input_at(0)],
outputs=[model.get_layer('resnet50').get_output_at(0)])
train_predict(model, target_train_path, pid_path, score_path)
ll = [[[1, 0.5, 0.9, 0, 0.3], [0.5, 0, 0, 0, 1]]]
q_att = np.array([[[1, 1] + [1] * 5, [1] * 7]])
d_att = np.ones((1, 5, 7))
d_att[0, 3:, :] = 0
# 1)
print 'q attention'
print q_att
print 'd attention'
print d_att
trans_mtx = np.array(ll)
print trans_mtx
# 2) + 4)
kp = Model(inputs=[
att_knrm.l_field_translation[0], att_knrm.l_q_att_in,
att_knrm.l_field_att_in[0]
],
outputs=att_knrm.l_d_layer[0])
kp_res = kp.predict([trans_mtx, q_att, d_att])
print 'raw kernel scores with attention'
print kp_res.shape
print kp_res
print 'first kernel scores'
print kp_res[0, :, :, 0]
# 3)
kp = Model(inputs=[
att_knrm.l_field_translation[0], att_knrm.l_q_att_in,
att_knrm.l_field_att_in[0]
],
outputs=att_knrm.kp_logsum(att_knrm.l_d_layer[0]))
def extract_features(input_dir,
output_dir,
model_type='inceptionv3',
batch_size=32):
"""
Extracts features from a CNN trained on ImageNet classification from all
videos in a directory.
Args:
input_dir (str): Input directory of videos to extract from.
output_dir (str): Directory where features should be stored.
model_type (str): Model type to use.
batch_size (int): Batch size to use when processing.
"""
input_dir = os.path.expanduser(input_dir)
output_dir = os.path.expanduser(output_dir)
if not os.path.isdir(input_dir):
sys.stderr.write("Input directory '%s' does not exist!\n" % input_dir)
sys.exit(1)
# Load desired ImageNet model
# Note: import Keras only when needed so we don't waste time revving up
# Theano/TensorFlow needlessly in case of an error
model = None
input_shape = (224, 224)
shape = input_shape
if model_type.lower() == 'inceptionv3':
from keras.applications import InceptionV3
model = InceptionV3(include_top=True, weights='imagenet')
elif model_type.lower() == 'xception':
from keras.applications import Xception
model = Xception(include_top=True, weights='imagenet')
elif model_type.lower() == 'resnet50':
from keras.applications import ResNet50
model = ResNet50(include_top=True, weights='imagenet')
elif model_type.lower() == 'vgg16':
from keras.applications import VGG16
model = VGG16(include_top=True, weights='imagenet')
elif model_type.lower() == 'vgg19':
from keras.applications import VGG19
model = VGG19(include_top=True, weights='imagenet')
elif model_type.lower() == 'vggface':
from keras.engine import Model
from keras.layers import Input
from keras_vggface.vggface import VGGFace
model = VGGFace(include_top=True) # pooling: None, avg or max
else:
sys.stderr.write("'%s' is not a valid ImageNet model.\n" % model_type)
sys.exit(1)
if model_type.lower() == 'inceptionv3' or model_type.lower() == 'xception':
shape = (299, 299)
# Get outputs of model from layer just before softmax predictions
from keras.models import Model
model = Model(model.inputs, output=model.layers[-2].output)
# Create output directories
visual_dir = output_dir # RGB features
#motion_dir = os.path.join(output_dir, 'motion') # Spatiotemporal features
#opflow_dir = os.path.join(output_dir, 'opflow') # Optical flow features
for directory in [visual_dir]: #, motion_dir, opflow_dir]:
if not os.path.exists(directory):
os.makedirs(directory)
# Find all videos that need to have features extracted
def is_video(x):
return x.endswith('.mp4') or x.endswith('.avi') or x.endswith('.mov')
vis_existing = [x.split('.')[0] for x in os.listdir(visual_dir)]
#mot_existing = [os.path.splitext(x)[0] for x in os.listdir(motion_dir)]
#flo_existing = [os.path.splitext(x)[0] for x in os.listdir(opflow_dir)]
video_filenames = [
x for x in sorted(os.listdir(input_dir))
if is_video(x) and os.path.splitext(x)[0] not in vis_existing
]
# Go through each video and extract features
from keras.applications.imagenet_utils import preprocess_input
for video_filename in tqdm(video_filenames):
# Open video clip for reading
try:
clip = VideoFileClip(os.path.join(input_dir, video_filename))
except Exception as e:
sys.stderr.write("Unable to read '%s'. Skipping...\n" %
video_filename)
sys.stderr.write("Exception: {}\n".format(e))
continue
# Sample frames at 1fps
fps = int(np.round(clip.fps))
frames = [
scipy.misc.imresize(crop_center(x.astype(np.float32)), shape)
for idx, x in enumerate(clip.iter_frames())
]
n_frames = len(frames)
frames_arr = np.empty((n_frames, ) + shape + (3, ), dtype=np.float32)
for idx, frame in enumerate(frames):
frames_arr[idx, :, :, :] = frame
frames_arr = preprocess_input(frames_arr)
features = model.predict(frames_arr, batch_size=batch_size)
name, _ = os.path.splitext(video_filename)
feat_filepath = os.path.join(visual_dir, name + '.npy')
with open(feat_filepath, 'wb') as f:
np.save(f, features)
def build_model(embeddings):
# input representation features
words_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
pos1_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
pos2_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
segs_input = Input(shape=[SEQUENCE_LEN, 3], dtype='float32')
# lexical features
e1_input = Input(shape=[ENTITY_LEN], dtype='int32') # L1
e2_input = Input(shape=[ENTITY_LEN], dtype='int32') # L2
e1context_input = Input(shape=[2], dtype='int32') # L3
e2context_input = Input(shape=[2], dtype='int32') # L4
# word embedding
we = embeddings["word_embeddings"]
words_embed = Embedding(we.shape[0], we.shape[1], weights=[we])
words = words_embed(words_input)
e1 = words_embed(e1_input)
e2 = words_embed(e2_input)
e1context = words_embed(e1context_input)
e2context = words_embed(e2context_input)
# lexical feature
e1_flat = Flatten()(e1)
e2_flat = Flatten()(e2)
e1context_flat = Flatten()(e1context)
e2context_flat = Flatten()(e2context)
# position embedding
pe1 = embeddings["position_embeddings_1"]
pos1 = Embedding(pe1.shape[0], pe1.shape[1], weights=[pe1])(pos1_input)
pe2 = embeddings["position_embeddings_2"]
pos2 = Embedding(pe2.shape[0], pe2.shape[1], weights=[pe2])(pos2_input)
# input representation
input_repre = Concatenate()([words, pos1, pos2])
input_repre = Dropout(DROPOUT)(input_repre)
# input attention
e1_repeat = RepeatVector(SEQUENCE_LEN)(e1_flat)
e2_repeat = RepeatVector(SEQUENCE_LEN)(e2_flat)
concat = Concatenate()([words, e1_repeat, e2_repeat])
alpha = Dense(1, activation="softmax")(concat)
alpha = Reshape([SEQUENCE_LEN])(alpha)
alpha = RepeatVector(WORD_REPRE_SIZE)(alpha)
alpha = Permute([2, 1])(alpha)
input_repre = Multiply()([input_repre, alpha])
# word-level convolution
input_conved = Conv1D(filters=NB_FILTERS_WORD,
kernel_size=WINDOW_SIZE_WORD,
padding="same",
activation="relu",
kernel_initializer=TruncatedNormal(stddev=0.1),
bias_initializer=Constant(0.1))(input_repre)
input_pooled = PiecewiseMaxPool()([input_conved, segs_input])
# fully connected
outputs = [input_pooled, e1_flat, e2_flat, e1context_flat, e2context_flat]
output = Concatenate()(outputs)
output = Dropout(DROPOUT)(output)
output = Dense(
units=NB_RELATIONS,
activation="softmax",
kernel_initializer=TruncatedNormal(stddev=0.1),
bias_initializer=Constant(0.1),
kernel_regularizer='l2',
bias_regularizer='l2',
)(output)
model = Model(inputs=[
words_input, pos1_input, pos2_input, e1_input, e2_input,
e1context_input, e2context_input, segs_input
],
outputs=[output])
model.compile(loss="sparse_categorical_crossentropy",
optimizer='sgd',
metrics=['accuracy'])
# model.summary()
return model
def att_res_ds_unet_model(input_shape=(4, 128, 128, 128),
n_base_filters=16,
depth=5,
dropout_rate=0.3,
n_segmentation_levels=3,
n_labels=4,
optimizer=Adam,
initial_learning_rate=5e-4,
loss_function=weighted_dice_coefficient_loss,
activation_name="sigmoid"):
"""
This function builds a model proposed by Isensee et al. for the BRATS 2017 competition:
https://www.cbica.upenn.edu/sbia/Spyridon.Bakas/MICCAI_BraTS/MICCAI_BraTS_2017_proceedings_shortPapers.pdf
This network is highly similar to the model proposed by Kayalibay et al. "CNN-based Segmentation of Medical
Imaging Data", 2017: https://arxiv.org/pdf/1701.03056.pdf
:param input_shape:
:param n_base_filters:
:param depth:
:param dropout_rate:
:param n_segmentation_levels:
:param n_labels:
:param optimizer:
:param initial_learning_rate:
:param loss_function:
:param activation_name:
:return:
"""
inputs = Input(input_shape)
current_layer = inputs
# 每个深度的输出
level_output_layers = list()
level_filters = list()
for level_number in range(depth): # depth=5; [0,1,2,3,4]
# Encoder结构构建 (残差)
n_level_filters = (2**
level_number) * n_base_filters # 2^level_num * 16
level_filters.append(n_level_filters)
# convolution_block：继承自原始unet，卷积->(正则)->激活(ReLU/LeakyReLU)
if current_layer is inputs:
in_conv = create_convolution_block(
current_layer, n_level_filters) # 第一层通道数*4，尺寸不变
else:
in_conv = create_convolution_block(current_layer,
n_level_filters,
strides=(2, 2, 2)) # 通道数*2，尺寸减半
# 残差单元：conv_block->dropout->conv_block
context_output_layer = create_context_module(in_conv,
n_level_filters,
dropout_rate=dropout_rate)
# 残差模块：残差单元+in_conv
summation_layer = Add()([in_conv, context_output_layer])
level_output_layers.append(summation_layer)
current_layer = summation_layer
segmentation_layers = list()
for level_number in range(depth - 2, -1, -1): # [3,2,1,0]
# attention
gating = gating_signal(level_output_layers[level_number + 1],
level_filters[level_number], True)
att = attention_block(level_output_layers[level_number], gating,
level_filters[level_number])
# 上采样
# 上采样放大一倍，卷积减少一半通道->conv_block
up_sampling = create_up_sampling_module(current_layer,
level_filters[level_number])
# concat：skip connection
# concatenation_layer = concatenate([level_output_layers[level_number], up_sampling], axis=1)
concatenation_layer = concatenate([att, up_sampling], axis=1)
# concat后两次卷积channel减半
localization_output = create_localization_module(
concatenation_layer, level_filters[level_number])
current_layer = localization_output
if level_number < n_segmentation_levels: # <3; [2,1,0]时记录
# 记录层
segmentation_layers.insert(
0,
Conv3D(n_labels, (1, 1, 1))(current_layer))
output_layer = None
for level_number in reversed(range(n_segmentation_levels)):
segmentation_layer = segmentation_layers[level_number]
if output_layer is None:
output_layer = segmentation_layer
else:
output_layer = Add()([output_layer, segmentation_layer])
if level_number > 0:
output_layer = UpSampling3D(size=(2, 2, 2))(output_layer)
# sigmoid激活输出
activation_block = Activation(activation_name)(output_layer)
model = Model(inputs=inputs, outputs=activation_block)
model.compile(optimizer=optimizer(lr=initial_learning_rate),
loss=loss_function)
# 返回模型
return model
def unet_model_3d(input_shape, pool_size=(2, 2, 2), n_labels=1, initial_learning_rate=0.00001, deconvolution=False,
depth=4, n_base_filters=32, include_label_wise_dice_coefficients=False, metrics=dice_coefficient,
batch_normalization=False, activation_name="sigmoid"):
"""
Builds the 3D UNet Keras model.f
:param metrics: List metrics to be calculated during model training (default is dice coefficient).
:param include_label_wise_dice_coefficients: If True and n_labels is greater than 1, model will report the dice
coefficient for each label as metric.
:param n_base_filters: The number of filters that the first layer in the convolution network will have. Following
layers will contain a multiple of this number. Lowering this number will likely reduce the amount of memory required
to train the model.
:param depth: indicates the depth of the U-shape for the model. The greater the depth, the more max pooling
layers will be added to the model. Lowering the depth may reduce the amount of memory required for training.
:param input_shape: Shape of the input data (n_chanels, x_size, y_size, z_size). The x, y, and z sizes must be
divisible by the pool size to the power of the depth of the UNet, that is pool_size^depth.
:param pool_size: Pool size for the max pooling operations.
:param n_labels: Number of binary labels that the model is learning.
:param initial_learning_rate: Initial learning rate for the model. This will be decayed during training.
:param deconvolution: If set to True, will use transpose convolution(deconvolution) instead of up-sampling. This
increases the amount memory required during training.
:return: Untrained 3D UNet Model
"""
inputs = Input(input_shape)
current_layer = inputs
levels = list()
# add levels with max pooling
for layer_depth in range(depth):
layer1 = create_convolution_block(input_layer=current_layer, n_filters=n_base_filters*(2**layer_depth),
batch_normalization=batch_normalization)
layer2 = create_convolution_block(input_layer=layer1, n_filters=n_base_filters*(2**layer_depth)*2,
batch_normalization=batch_normalization)
if layer_depth < depth - 1:
current_layer = MaxPooling3D(pool_size=pool_size)(layer2)
levels.append([layer1, layer2, current_layer])
else:
current_layer = layer2
levels.append([layer1, layer2])
# add levels with up-convolution or up-sampling
for layer_depth in range(depth-2, -1, -1):
up_convolution = get_up_convolution(pool_size=pool_size, deconvolution=deconvolution,
n_filters=current_layer._keras_shape[1])(current_layer)
concat = concatenate([up_convolution, levels[layer_depth][1]], axis=1)
current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=concat, batch_normalization=batch_normalization)
current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
input_layer=current_layer,
batch_normalization=batch_normalization)
final_convolution = Conv3D(n_labels, (1, 1, 1))(current_layer)
act = Activation(activation_name)(final_convolution)
model = Model(inputs=inputs, outputs=act)
if not isinstance(metrics, list):
metrics = [metrics]
if include_label_wise_dice_coefficients and n_labels > 1:
label_wise_dice_metrics = [get_label_dice_coefficient_function(index) for index in range(n_labels)]
if metrics:
metrics = metrics + label_wise_dice_metrics
else:
metrics = label_wise_dice_metrics
model.compile(optimizer=Adam(lr=initial_learning_rate), loss=dice_coefficient_loss, metrics=metrics)
return model
def isensee2017_model(input_shape=(4, 128, 128, 128),
n_base_filters=16,
depth=5,
dropout_rate=0.3,
n_segmentation_levels=3,
n_labels=4,
optimizer=Adam,
initial_learning_rate=5e-4,
loss_function=weighted_dice_coefficient_loss,
activation_name="sigmoid"):
"""
This function builds a model proposed by Isensee et al. for the BRATS 2017 competition:
https://www.cbica.upenn.edu/sbia/Spyridon.Bakas/MICCAI_BraTS/MICCAI_BraTS_2017_proceedings_shortPapers.pdf
This network is highly similar to the model proposed by Kayalibay et al. "CNN-based Segmentation of Medical
Imaging Data", 2017: https://arxiv.org/pdf/1701.03056.pdf
:param input_shape:
:param n_base_filters:
:param depth:
:param dropout_rate:
:param n_segmentation_levels:
:param n_labels:
:param optimizer:
:param initial_learning_rate:
:param loss_function:
:param activation_name:
:return:
"""
inputs = Input(input_shape)
current_layer = inputs
level_output_layers = list()
level_filters = list()
for level_number in range(depth):
n_level_filters = (2**level_number) * n_base_filters
level_filters.append(n_level_filters)
if current_layer is inputs:
in_conv = create_convolution_block(current_layer, n_level_filters)
else:
in_conv = create_convolution_block(current_layer,
n_level_filters,
strides=(2, 2, 2))
context_output_layer = create_context_module(in_conv,
n_level_filters,
dropout_rate=dropout_rate)
summation_layer = Add()([in_conv, context_output_layer])
level_output_layers.append(summation_layer)
current_layer = summation_layer
segmentation_layers = list()
for level_number in range(depth - 2, -1, -1):
up_sampling = create_up_sampling_module(current_layer,
level_filters[level_number])
concatenation_layer = concatenate(
[level_output_layers[level_number], up_sampling], axis=1)
localization_output = create_localization_module(
concatenation_layer, level_filters[level_number])
current_layer = localization_output
if level_number < n_segmentation_levels:
segmentation_layers.insert(
0,
create_convolution_block(current_layer,
n_filters=n_labels,
kernel=(1, 1, 1)))
output_layer = None
for level_number in reversed(range(n_segmentation_levels)):
segmentation_layer = segmentation_layers[level_number]
if output_layer is None:
output_layer = segmentation_layer
else:
output_layer = Add()([output_layer, segmentation_layer])
if level_number > 0:
output_layer = UpSampling3D(size=(2, 2, 2))(output_layer)
activation_block = Activation(activation_name)(output_layer)
model = Model(inputs=inputs, outputs=activation_block)
model.compile(optimizer=optimizer(lr=initial_learning_rate),
loss=loss_function)
return model
def make(self, theano_kwargs=None):
'''Make the model and compile it.
Igor's config options control everything.
Arg:
theano_kwargs as dict for debugging theano or submitting something custom
'''
if self.igor.embedding_type == "convolutional":
make_convolutional_embedding(self.igor)
elif self.igor.embedding_type == "token":
make_token_embedding(self.igor)
elif self.igor.embedding_type == "shallowconv":
make_shallow_convolutional_embedding(self.igor)
elif self.igor.embedding_type == "minimaltoken":
make_minimal_token_embedding(self.igor)
else:
raise Exception("Incorrect embedding type")
B = self.igor.batch_size
spine_input_shape = (B, self.igor.max_num_supertags)
child_input_shape = (B, 1)
parent_input_shape = (B, 1)
E, V = self.igor.word_embedding_size, self.igor.word_vocab_size # for word embeddings
repeat_N = self.igor.max_num_supertags # for lex
mlp_size = self.igor.mlp_size
## dropout parameters
p_emb = self.igor.p_emb_dropout
p_W = self.igor.p_W_dropout
p_U = self.igor.p_U_dropout
w_decay = self.igor.weight_decay
p_mlp = self.igor.p_mlp_dropout
def predict_params():
return {
'output_dim': 1,
'W_regularizer': l2(w_decay),
'activation': 'relu',
'b_regularizer': l2(w_decay)
}
dspineset_in = Input(batch_shape=spine_input_shape,
name='daughter_spineset_in',
dtype='int32')
pspineset_in = Input(batch_shape=spine_input_shape,
name='parent_spineset_in',
dtype='int32')
dhead_in = Input(batch_shape=child_input_shape,
name='daughter_head_input',
dtype='int32')
phead_in = Input(batch_shape=parent_input_shape,
name='parent_head_input',
dtype='int32')
dspine_in = Input(batch_shape=child_input_shape,
name='daughter_spine_input',
dtype='int32')
inputs = [dspineset_in, pspineset_in, dhead_in, phead_in, dspine_in]
### Layer functions
############# Convert the word indices to vectors
F_embedword = Embedding(input_dim=V,
output_dim=E,
mask_zero=True,
W_regularizer=l2(w_decay),
dropout=p_emb)
if self.igor.saved_embeddings is not None:
self.logger.info("+ Cached embeddings loaded")
F_embedword.initial_weights = [self.igor.saved_embeddings]
###### Prediction Functions
## these functions learn a vector which turns a tensor into a matrix of probabilities
### P(Parent supertag | Child, Context)
F_parent_predict = ProbabilityTensor(
name='parent_predictions',
dense_function=Dense(**predict_params()))
### P(Leaf supertag)
F_leaf_predict = ProbabilityTensor(
name='leaf_predictions', dense_function=Dense(**predict_params()))
###### Network functions.
##### Input word, correct its dimensions (basically squash in a certain way)
F_singleword = compose(Fix(), F_embedword)
##### Input spine, correct diemnsions, broadcast across 1st dimension
F_singlespine = compose(RepeatVector(repeat_N), Fix(),
self.igor.F_embedspine)
##### Concatenate and map to a single space
F_alignlex = compose(
RepeatVector(repeat_N), Dropout(p_mlp),
Dense(mlp_size, activation='relu', name='dense_align_lex'), concat)
F_alignall = compose(
Distribute(Dropout(p_mlp), name='distribute_align_all_dropout'),
Distribute(Dense(mlp_size,
activation='relu',
name='align_all_dense'),
name='distribute_align_all_dense'), concat)
F_alignleaf = compose(
Distribute(
Dropout(p_mlp * 0.66), name='distribute_leaf_dropout'
), ### need a separate oen because the 'concat' is different for the two situations
Distribute(Dense(mlp_size, activation='relu', name='leaf_dense'),
name='distribute_leaf_dense'),
concat)
### embed and form all of the inputs into their components
### note: spines == supertags. early word choice, haven't refactored.
leaf_spines = self.igor.F_embedspine(dspineset_in)
pspine_context = self.igor.F_embedspine(pspineset_in)
dspine_single = F_singlespine(dspine_in)
dhead = F_singleword(dhead_in)
phead = F_singleword(phead_in)
### combine the lexical material
lexical_context = F_alignlex([dhead, phead])
#### P(Parent Supertag | Daughter Supertag, Lexical Context)
### we know the daughter spine, want to know the parent spine
### size is (batch, num_supertags)
parent_problem = F_alignall(
[lexical_context, dspine_single, pspine_context])
### we don't have the parent, we just have a leaf
leaf_problem = F_alignleaf([lexical_context, leaf_spines])
parent_predictions = F_parent_predict(parent_problem)
leaf_predictions = F_leaf_predict(leaf_problem)
predictions = [parent_predictions, leaf_predictions]
theano_kwargs = theano_kwargs or {}
## make it quick so i can load in the weights.
self.model = Model(input=inputs,
output=predictions,
preloaded_data=self.igor.preloaded_data,
**theano_kwargs)
#mask_cache = traverse_nodes(parent_prediction)
#desired_masks = ['merge_3.in.mask.0']
#self.p_tensor = K.function(inputs+[K.learning_phase()], [parent_predictions, F_parent_predict.inbound_nodes[0].input_masks[0]])
if self.igor.from_checkpoint:
self.load_checkpoint_weights()
elif not self.igor.in_training:
raise Exception("No point in running this without trained weights")
if not self.igor.in_training:
expanded_children = RepeatVector(repeat_N, axis=2)(leaf_spines)
expanded_parent = RepeatVector(repeat_N, axis=1)(pspine_context)
expanded_lex = RepeatVector(repeat_N, axis=1)(
lexical_context
) # axis here is arbitary; its repeating on 1 and 2, but already repeated once
huge_tensor = concat(
[expanded_lex, expanded_children, expanded_parent])
densely_aligned = LastDimDistribute(
F_alignall.get(1).layer)(huge_tensor)
output_predictions = Distribute(
F_parent_predict, force_reshape=True)(densely_aligned)
primary_inputs = [phead_in, dhead_in, pspineset_in, dspineset_in]
leaf_inputs = [phead_in, dhead_in, dspineset_in]
self.logger.info("+ Compiling prediction functions")
self.inner_func = K.Function(primary_inputs + [K.learning_phase()],
output_predictions)
self.leaf_func = K.Function(leaf_inputs + [K.learning_phase()],
leaf_predictions)
try:
self.get_ptensor = K.function(
primary_inputs + [K.learning_phase()], [
output_predictions,
])
except:
import pdb
pdb.set_trace()
else:
optimizer = Adam(self.igor.LR,
clipnorm=self.igor.max_grad_norm,
clipvalue=self.igor.grad_clip_threshold)
theano_kwargs = theano_kwargs or {}
self.model.compile(loss="categorical_crossentropy",
optimizer=optimizer,
metrics=['accuracy'],
**theano_kwargs)
def MobileUNet(input_shape=None,
alpha=1.0,
alpha_up=1.0,
depth_multiplier=1,
dropout=1e-3,
input_tensor=None,
weight_decay=1e-5):
if input_tensor is None:
img_input = Input(shape=input_shape)
else:
if not K.is_keras_tensor(input_tensor):
img_input = Input(tensor=input_tensor, shape=input_shape)
else:
img_input = input_tensor
b00 = _conv_block(img_input, 32, alpha, strides=(4, 4), block_id=0)
b01 = _depthwise_conv_block(b00, 64, alpha, depth_multiplier, block_id=1)
b02 = _depthwise_conv_block(b01, 128, alpha, depth_multiplier, block_id=2, strides=(2, 2))
b03 = _depthwise_conv_block(b02, 128, alpha, depth_multiplier, block_id=3)
b04 = _depthwise_conv_block(b03, 256, alpha, depth_multiplier, block_id=4, strides=(2, 2))
b05 = _depthwise_conv_block(b04, 256, alpha, depth_multiplier, block_id=5)
b06 = _depthwise_conv_block(b05, 512, alpha, depth_multiplier, block_id=6, strides=(2, 2))
b07 = _depthwise_conv_block(b06, 512, alpha, depth_multiplier, block_id=7)
b08 = _depthwise_conv_block(b07, 512, alpha, depth_multiplier, block_id=8)
b09 = _depthwise_conv_block(b08, 512, alpha, depth_multiplier, block_id=9)
b10 = _depthwise_conv_block(b09, 512, alpha, depth_multiplier, block_id=10)
b11 = _depthwise_conv_block(b10, 512, alpha, depth_multiplier, block_id=11)
b12 = _depthwise_conv_block(b11, 1024, alpha, depth_multiplier, block_id=12, strides=(2, 2))
b13 = _depthwise_conv_block(b12, 1024, alpha, depth_multiplier, block_id=13)
# b13 = Dropout(dropout)(b13)
filters = int(512 * alpha)
up1 = concatenate([
Conv2DTranspose(filters, (2, 2), strides=(2, 2), padding='same',
kernel_regularizer=regu.l2(weight_decay),
bias_regularizer=regu.l2(weight_decay))(b13),
b11,
], axis=3)
b14 = _depthwise_conv_block(up1, filters, alpha_up, depth_multiplier, block_id=14)
filters = int(256 * alpha)
up2 = concatenate([
Conv2DTranspose(filters, (2, 2), strides=(2, 2), padding='same',
kernel_regularizer=regu.l2(weight_decay),
bias_regularizer=regu.l2(weight_decay))(b14),
b05,
], axis=3)
b15 = _depthwise_conv_block(up2, filters, alpha_up, depth_multiplier, block_id=15)
filters = int(128 * alpha)
up3 = concatenate([
Conv2DTranspose(filters, (2, 2), strides=(2, 2), padding='same',
kernel_regularizer=regu.l2(weight_decay),
bias_regularizer=regu.l2(weight_decay))(b15),
b03,
], axis=3)
b16 = _depthwise_conv_block(up3, filters, alpha_up, depth_multiplier, block_id=16)
filters = int(64 * alpha)
up4 = concatenate([
Conv2DTranspose(filters, (2, 2), strides=(2,2), padding='same',
kernel_regularizer=regu.l2(weight_decay),
bias_regularizer=regu.l2(weight_decay))(b16),
b01,
], axis=3)
b17 = _depthwise_conv_block(up4, filters, alpha_up, depth_multiplier, block_id=17)
filters = int(32 * alpha)
up5 = concatenate([b17, b00], axis=3)
# b18 = _depthwise_conv_block(up5, filters, alpha_up, depth_multiplier, block_id=18)
b18 = _conv_block(up5, filters, alpha_up, block_id=18)
logits = Conv2D(1, (1, 1), kernel_initializer='he_normal', activation='linear',
kernel_regularizer=regu.l2(weight_decay),
bias_regularizer=regu.l2(weight_decay))(b18)
logits = BilinearUpSampling2D(size=(4, 4),name='logits')(logits)
proba = Activation('sigmoid', name='proba')(logits)
model = Model(img_input, [logits,proba])
return model
def cnn_model(embedding_weights, cv_dat, max_len, model_w, lda, dictionary,
idx2word, alpha):
max_len = 1000 if max_len > 1000 else max_len
#max_len = 1000
dropout = 0.8
print max_len
json_file = open(model_w + 'model.json', 'r')
loaded_model_json = json_file.read()
json_file.close()
model_lda = model_from_json(loaded_model_json)
# load weights into new model
#print layer_dict
train_x, test_x, train_y, test_y = cv_dat
test_lda = get_alpha(test_x, lda, dictionary, idx2word)
print "Maximum length of sentence:" + str(max_len)
print "Distribution of labels in training set:"
print Counter([np.argmax(dat) for dat in train_y])
print "Distribution of labels in testing set:"
print Counter([np.argmax(dat) for dat in test_y])
test_x = np.array(sequence.pad_sequences(test_x, maxlen=max_len),
dtype=np.int)
#print (train_x.shape)
#print train_y.shape
train_x, val_x, train_y, val_y = train_test_split(train_x,
train_y,
test_size=0.166,
random_state=666,
stratify=train_y)
train_lda = get_alpha(train_x, lda, dictionary, idx2word)
val_lda = get_alpha(val_x, lda, dictionary, idx2word)
#defining the model architecture now
train_x = np.array(sequence.pad_sequences(train_x, maxlen=max_len),
dtype=np.int)
val_x = np.array(sequence.pad_sequences(val_x, maxlen=max_len),
dtype=np.int)
review_text = Input(shape=(max_len, ), dtype='int64', name="body_input")
embedded_layer_body = Embedding(embedding_weights.shape[0],
embedding_weights.shape[1],
mask_zero=False,
input_length=max_len,
weights=[embedding_weights],
trainable=True)(review_text)
lda_input = Input(shape=(30, ), dtype='float32', name="lda_inp")
#load the weights from pre-trained model
lrelu = LeakyReLU(alpha=0.1)
conv1 = Conv1D(filters=128,
kernel_size=1,
padding='same',
activation=lrelu,
weights=layer_dict['conv1d_1'].get_weights())
conv2 = Conv1D(filters=128,
kernel_size=3,
padding='same',
activation=lrelu,
weights=layer_dict['conv1d_2'].get_weights())
conv3 = Conv1D(filters=128,
kernel_size=5,
padding='same',
activation=lrelu,
weights=layer_dict['conv1d_3'].get_weights())
#conv1 = Conv1D(filters=128, kernel_size=1, padding='same', activation='relu')
#conv2 = Conv1D(filters=128, kernel_size=3, padding='same', activation='relu')
#conv3 = Conv1D(filters=128, kernel_size=5, padding='same', activation='relu')
conv1a = conv1(embedded_layer_body)
glob1a = GlobalAveragePooling1D()(conv1a)
#max1 = AveragePooling1D()(conv1a)
conv2a = conv2(embedded_layer_body)
glob2a = GlobalAveragePooling1D()(conv2a)
#max2 = AveragePooling1D()(conv2a)
conv3a = conv3(embedded_layer_body)
glob3a = GlobalAveragePooling1D()(conv3a)
#max3 = AveragePooling1D()(conv3a)
merge_pooling = concatenate([glob1a, glob2a, glob3a])
#merge_pooling = concatenate([max1, max2, max3])
hidden_layer = Dense(1200,
activation='tanh',
kernel_initializer="glorot_uniform")(merge_pooling)
#hidden_concat = concatenate([hidden_layer, lda_vec])
dropout_hidden = Dropout(dropout)(hidden_layer)
#merge_hidden = concatenate([dropout_hidden, lda_input])
batch_norm = BatchNormalization()(dropout_hidden)
#hidden_layer_2 = Dense(600, activation='tanh', kernel_initializer="glorot_uniform")(batch_norm)
#dropout_hidden_2 = Dropout(0.6)(hidden_layer_2)
#batch_n_2 = BatchNormalization()(dropout_hidden_2)
hidden_layer_3 = Dense(600,
activation='tanh',
kernel_initializer="glorot_uniform")(batch_norm)
dropout_hidden_3 = Dropout(0.5)(hidden_layer_3)
batch_n_3 = BatchNormalization()(dropout_hidden_3)
output_layer = Dense(2, activation='softmax', name='out_sent')(batch_n_3)
output_lda = Dense(30, activation='softmax', name='out_lda')(batch_n_3)
model = Model([review_text], output=[output_layer, output_lda])
layer_dict_nu = dict([(layer.name, layer) for layer in model.layers])
adam = Adam(lr=0.001)
model.compile(
loss=['categorical_crossentropy', 'kullback_leibler_divergence'],
optimizer=adam,
metrics=['accuracy'],
loss_weights={
'out_sent': (1 - alpha),
'out_lda': alpha
})
#model.compile(loss=ncce, optimizer=adam, metrics=['accuracy'])
earlystop = EarlyStopping(monitor='val_out_sent_loss',
min_delta=0.0001,
patience=9,
verbose=1,
mode='auto')
callbacks_list = [earlystop]
print model.summary()
model.fit([train_x], [train_y, train_lda],
batch_size=32 * 2,
epochs=50,
verbose=1,
shuffle=True,
callbacks=callbacks_list,
validation_data=[[val_x], [val_y, val_lda]])
#model.fit([train_x, train_lda], [train_y, train_lda], batch_size=64, epochs=25,
# verbose=1, shuffle=True)
test_predictions = model.predict([test_x], verbose=False)
#test_y = [np.argmax(pred) for pred in test_y]
test_pred = [np.argmax(pred) for pred in test_predictions[0]]
#print test_pred
test_y = [np.argmax(label) for label in test_y]
error_preds = [
i for i in range(0, len(test_pred)) if (test_y[i] != test_pred[i])
]
print len(error_preds)
misclassified = [test_x[i] for i in error_preds]
misclassified = [[get_id2word(idx, idx2word) for idx in sent if idx != 0]
for sent in misclassified]
labels = [(test_y[i], test_pred[i]) for i in error_preds]
#acc = accuracy_score(test_y, test_pred)
print acc
return acc, misclassified, labels
def unet_model_3d(input_shape,
n_labels,
batch_normalization=False,
initial_learning_rate=0.00001,
metrics=m.dice_coef):
"""
input_shape:without batch_size,(img_height,img_width,img_depth)
metrics:
"""
inputs = Input(input_shape)
down_layer = []
layer = inputs
# down_layer_1
layer = res_block_v2_3d(layer, 32, batch_normalization=batch_normalization)
down_layer.append(layer)
layer = MaxPooling3D(pool_size=[2, 2, 2],
strides=[2, 2, 2],
padding='same')(layer)
print(str(layer.get_shape()))
# down_layer_2
layer = res_block_v2_3d(layer, 64, batch_normalization=batch_normalization)
down_layer.append(layer)
layer = MaxPooling3D(pool_size=[2, 2, 2],
strides=[2, 2, 2],
padding='same')(layer)
print(str(layer.get_shape()))
# down_layer_3
layer = res_block_v2_3d(layer,
128,
batch_normalization=batch_normalization)
down_layer.append(layer)
layer = MaxPooling3D(pool_size=[2, 2, 2],
strides=[2, 2, 2],
padding='same')(layer)
print(str(layer.get_shape()))
# down_layer_4
layer = res_block_v2_3d(layer,
256,
batch_normalization=batch_normalization)
down_layer.append(layer)
layer = MaxPooling3D(pool_size=[2, 2, 2],
strides=[2, 2, 2],
padding='same')(layer)
print(str(layer.get_shape()))
# bottle_layer
layer = res_block_v2_3d(layer,
512,
batch_normalization=batch_normalization)
print(str(layer.get_shape()))
# up_layer_4
layer = up_and_concate_3d(layer, down_layer[3])
layer = res_block_v2_3d(layer,
256,
batch_normalization=batch_normalization)
print(str(layer.get_shape()))
# up_layer_3
layer = up_and_concate_3d(layer, down_layer[2])
layer = res_block_v2_3d(layer,
128,
batch_normalization=batch_normalization)
print(str(layer.get_shape()))
# up_layer_2
layer = up_and_concate_3d(layer, down_layer[1])
layer = res_block_v2_3d(layer, 64, batch_normalization=batch_normalization)
print(str(layer.get_shape()))
# up_layer_1
layer = up_and_concate_3d(layer, down_layer[0])
layer = res_block_v2_3d(layer, 32, batch_normalization=batch_normalization)
print(str(layer.get_shape()))
# score_layer
layer = Conv3D(n_labels, [1, 1, 1], strides=[1, 1, 1])(layer)
print(str(layer.get_shape()))
# softmax
layer = Activation('softmax')(layer)
print(str(layer.get_shape()))
outputs = layer
model = Model(inputs=inputs, outputs=outputs)
metrics = [metrics]
model = multi_gpu_model(model, gpus=2)
model.summary()
model.compile(optimizer=Adam(lr=initial_learning_rate),
loss='categorical_crossentropy',
metrics=metrics)
return model
def unet_model_3d(input_shape, downsize_filters_factor=1, pool_size=(2, 2, 2), n_labels=1,
initial_learning_rate=0.00001, deconvolution=False):
"""
Builds the 3D UNet Keras model.
## ORIGINAL: :param input_shape: Shape of the input data (n_chanels, x_size, y_size, z_size).
## NOW: :param input_shape: Shape of the input data (x_size, y_size, z_size, n_chanels)
:param downsize_filters_factor: Factor to which to reduce the number of filters. Making this value larger will
reduce the amount of memory the model will need during training.
:param pool_size: Pool size for the max pooling operations.
:param n_labels: Number of binary labels that the model is learning.
:param initial_learning_rate: Initial learning rate for the model. This will be decayed during training.
:param deconvolution: If set to True, will use transpose convolution(deconvolution) instead of upsamping. This
increases the amount memory required during training.
:return: Untrained 3D UNet Model
"""
inputs = Input(input_shape)
conv1 = Conv3D(int(32/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(inputs)
conv1 = Conv3D(int(64/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv1)
pool1 = MaxPooling3D(pool_size=pool_size)(conv1)
conv2 = Conv3D(int(64/downsize_filters_factor), (1, 1, 1), activation='relu',
padding='same')(pool1)
conv2 = Conv3D(int(128/downsize_filters_factor), (1, 1, 1), activation='relu',
padding='same')(conv2)
"""
pool2 = MaxPooling3D(pool_size=pool_size)(conv2)
conv3 = Conv3D(int(128/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(pool2)
conv3 = Conv3D(int(256/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv3)
pool3 = MaxPooling3D(pool_size=pool_size)(conv3)
conv4 = Conv3D(int(256/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(pool3)
conv4 = Conv3D(int(512/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv4)
"""
"""
up5 = get_upconv(pool_size=pool_size, deconvolution=deconvolution, depth=2,
nb_filters=int(512/downsize_filters_factor), image_shape=input_shape[1:4])(conv4)
up5 = concatenate([up5, conv3], axis=-1)
conv5 = Conv3D(int(256/downsize_filters_factor), (3, 3, 3), activation='relu', padding='same')(up5)
conv5 = Conv3D(int(256/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv5)
up6 = get_upconv(pool_size=pool_size, deconvolution=deconvolution, depth=1,
nb_filters=int(256/downsize_filters_factor), image_shape=input_shape[1:4])(conv5)
up6 = concatenate([up6, conv2], axis=-1)
conv6 = Conv3D(int(128/downsize_filters_factor), (3, 3, 3), activation='relu', padding='same')(up6)
conv6 = Conv3D(int(128/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv6)
"""
up7 = get_upconv(pool_size=pool_size, deconvolution=deconvolution, depth=0,
nb_filters=int(128/downsize_filters_factor), image_shape=input_shape[1:4])(conv2)
up7 = concatenate([up7, conv1], axis=-1)
conv7 = Conv3D(int(64/downsize_filters_factor), (3, 3, 3), activation='relu', padding='same')(up7)
conv7 = Conv3D(int(64/downsize_filters_factor), (3, 3, 3), activation='relu',
padding='same')(conv7)
conv8 = Conv3D(n_labels, (1, 1, 1))(conv7)
# Shoudl be softmax?
act = Activation('softmax')(conv8)
model = Model(inputs=inputs, outputs=act)
model.compile(optimizer=Adam(lr=initial_learning_rate), loss=dice_coef_loss, metrics=[dice_coef])
model.summary()
return model
class BaseModel:
def __init__(self, use_development_set=True):
# used dirs
self.save_dir = "../saved_models/"
self.dir = "../example/"
self.embedding_dir = "../resource/embedding_matrix.pk"
self.entity_embedding_dir = "../resource/entity_type_matrix.pk"
self.index_ids_file = "tri_index_ids.pk"
# some basic parameters of the model
self.model = None
self.max_len = 100
self.num_words = 6820
self.entity_type_num = 63
# pre-trained embeddings and their parameters.
self.embedding_matrix = BaseModel.load_pickle(self.embedding_dir)
self.entity_embedding_matrix = BaseModel.load_pickle(
self.entity_embedding_dir)
self.embedding_trainable = False
self.EMBEDDING_DIM = 200
self.ENTITY_TYPE_VEC_DIM = 50
# inputs to the model
self.use_development_set = use_development_set
self.train_word_inputs, self.train_entity_inputs, self.train_labels, self.train_attention_labels = self.load_data(
train=True)
self.test_word_inputs, self.test_entity_inputs, self.test_labels, self.test_attention_labels = self.load_data(
train=False)
self.dev_word_inputs, self.dev_entity_inputs, self.dev_labels, self.dev_attention_labels = [
None, None, None, None
]
# if you want to use development, this part can help you to split the development set from the train set.
if self.use_development_set:
self.split_train_set()
# dict used to calculate the F1
self.index_ids = BaseModel.load_pickle(self.dir + self.index_ids_file)
self.sen_input, self.entity_type_input = None, None
self.sen_embedding, self.entity_embedding = None, None
self.output = None
def build_model(self):
pass
def train_model(self):
pass
def predict(self):
pass
def save_model(self, file=""):
self.model.save_weights(self.save_dir + file)
def load_data(self, train=True):
if train:
path = self.dir + "train_"
else:
path = self.dir + "test_"
rf = open(path + "input.pk", 'rb')
word_inputs = pickle.load(rf)
rf.close()
rf = open(path + "entity_inputs.pk", 'rb')
entity_inputs = pickle.load(rf)
rf.close()
rf = open(path + "labels.pk", 'rb')
labels = pickle.load(rf)
rf.close()
rf = open(path + "attention_label.pk", 'rb')
attention_labels = pickle.load(rf)
rf.close()
return word_inputs, entity_inputs, labels, attention_labels
@staticmethod
def load_pickle(file):
rf = open(file, 'rb')
embedding_matrix = pickle.load(rf)
rf.close()
return embedding_matrix
def split_train_set(self):
develop_doc_ids = self.load_pickle(self.dir + "development_doc_ids.pk")
sen_doc_ids = self.load_pickle(self.dir + "train_sen_doc_ids.pk")
train_index = []
develop_index = []
for index, doc_id in enumerate(sen_doc_ids):
if doc_id in develop_doc_ids:
develop_index.append(index)
else:
train_index.append(index)
self.dev_word_inputs = self.train_word_inputs[develop_index]
self.dev_entity_inputs = self.train_entity_inputs[develop_index]
self.dev_labels = self.train_labels[develop_index]
self.dev_attention_labels = self.train_attention_labels[develop_index]
self.train_word_inputs = self.train_word_inputs[train_index]
self.train_entity_inputs = self.train_entity_inputs[train_index]
self.train_labels = self.train_labels[train_index]
self.train_attention_labels = self.train_attention_labels[train_index]
print(np.shape(self.train_word_inputs))
print(np.shape(self.dev_word_inputs))
def compile_model(self):
self.sen_input, self.entity_type_input = self.make_input()
self.sen_embedding, self.entity_embedding = self.embedded()
self.output = self.build_model()
inputs = [self.sen_input, self.entity_type_input]
self.model = Model(inputs=inputs, outputs=self.output)
self.model.compile(optimizer='adam',
loss='categorical_crossentropy',
metrics=['acc'])
def make_input(self):
sentence = Input(shape=(self.max_len, ),
dtype='int32',
name='sentence_input')
entity_type = Input(shape=(self.max_len, ),
dtype='int32',
name='entity_type_input')
return sentence, entity_type
def embedded(self):
sentence_embedding_layer = Embedding(self.num_words + 2,
self.EMBEDDING_DIM,
weights=[self.embedding_matrix],
input_length=self.max_len,
trainable=False,
mask_zero=True)
sentence_embedding = sentence_embedding_layer(self.sen_input)
entity_embedding_layer = Embedding(
self.entity_type_num + 2,
self.ENTITY_TYPE_VEC_DIM,
weights=[self.entity_embedding_matrix],
input_length=self.max_len,
trainable=True,
mask_zero=True)
entity_embedding = entity_embedding_layer(self.entity_type_input)
return [sentence_embedding, entity_embedding]
embedded_sequences = embedding_layer(sequence_input)
cnns = []
for filter_length in filter_lengths:
x = Conv1D(nb_filter=nb_filter,
filter_length=filter_length,
border_mode='valid',
activation='relu',
W_constraint=maxnorm(3),
W_regularizer=l2(0.0001),
subsample_length=1)(embedded_sequences)
x = MaxPooling1D(pool_length=MAX_SEQUENCE_LENGTH - filter_length + 1)(x)
x = Flatten()(x)
cnns.append(x)
x = merge(cnns, mode='concat')
x = Dropout(0.2)(x)
x = Dense(128, activation='relu')(x)
preds = Dense(len(labels_index), activation='softmax')(x)
model = Model(sequence_input, preds)
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
# happy learning!
model.fit(x_train, y_train, validation_data=(x_val, y_val),
nb_epoch=5, batch_size=128)
def main():
args = get_args()
depth = args.depth
k = args.width
weight_file = args.weight_file
# load model and weights
img_size = 224
batch_size = 32
nb_class = 101
hidden_dim = 512
vgg_model = VGGFace(include_top=False, input_shape=(224, 224, 3))
last_layer = vgg_model.get_layer('pool5').output
x = Flatten(name='flatten')(last_layer)
x = Dense(hidden_dim, activation='relu', name='fc6')(x)
x = Dense(hidden_dim, activation='relu', name='fc7')(x)
out = Dense(nb_class, activation='softmax', name='fc8')(x)
model = Model(vgg_model.input, out)
model.load_weights(weight_file)
dataset_root = Path(__file__).parent.joinpath("appa-real",
"appa-real-release")
validation_image_dir = dataset_root.joinpath("test")
gt_valid_path = dataset_root.joinpath("gt_avg_test.csv")
image_paths = list(validation_image_dir.glob("*_face.jpg"))
faces = np.empty((batch_size, img_size, img_size, 3))
ages = []
image_names = []
for i, image_path in tqdm(enumerate(image_paths)):
faces[i % batch_size] = cv2.resize(cv2.imread(str(image_path), 1),
(img_size, img_size))
image_names.append(image_path.name[:-9])
if (i + 1) % batch_size == 0 or i == len(image_paths) - 1:
results = model.predict(faces)
ages_out = np.arange(0, 101).reshape(101, 1)
predicted_ages = results[1].dot(ages_out).flatten()
ages += list(predicted_ages)
print(len(ages))
print(len(image_names))
name2age = {image_names[i]: ages[i] for i in range(len(image_names))}
df = pd.read_csv(str(gt_valid_path))
appa_abs_error = 0.0
real_abs_error = 0.0
epsilon_error = 0.0
count1 = 0
count2 = 0
iter = 0
for i, row in df.iterrows():
#iter += 1
difference1 = name2age[row.file_name] - row.apparent_age_avg
difference2 = name2age[row.file_name] - row.real_age
appa_abs_error += abs(difference1)
real_abs_error += abs(difference2)
epsilon_error += error(name2age[row.file_name], row.apparent_age_avg,
0.3)
''''if int(difference1) == 0:
count1 += 1
if int(difference2) == 0:
count2 += 1
if iter < 5:
print("Predicted age: {}".format(name2age[row.file_name]))'''
print("MAE Apparent: {}".format(appa_abs_error / len(image_names)))
print("MAE Real: {}".format(real_abs_error / len(image_names)))
print("\u03B5-error: {}".format(epsilon_error / len(image_names)))
def _add_model(self):
nodes = self.nodes
config = self.model_config['PHM']
p = config['dropout_p']
mlp_l2 = config['l2']
D = config['mlp_output_dim']
activation = lambda x: relu(x, alpha=config['leaky_alpha'])
# SENTENCE LEVEL
# answer plus question
nodes['question_encoding_repeated'] = RepeatVector(self.answer_size)(nodes['question_encoding'])
nodes['answer_plus_question'] = merge([nodes['answer_encoding'], nodes['question_encoding_repeated']],
mode='sum')
# story mlp and dropout
ninputs, noutputs = ['story_encoding1'], ['story_encoding_mlp']
for ngram in config['ngram_inputs']:
ninputs.append('story_encoding1_%sgram' % ngram)
noutputs.append('story_encoding_mlp_%sgram' % ngram)
story_encoding_mlp = NTimeDistributed(Dense(D, init="identity", activation=activation,
W_regularizer=l2(mlp_l2),
trainable=config['trainable_story_encoding_mlp']))
for input, output in zip(ninputs, noutputs):
nodes[output] = story_encoding_mlp(self._get_node(input))
qa_encoding_mlp = NTimeDistributed(Dense(D, init="identity", activation=activation,
W_regularizer=l2(mlp_l2),
trainable=config['trainable_answer_plus_question_mlp']))
nodes['answer_plus_question_mlp'] = qa_encoding_mlp(nodes['answer_plus_question'])
nodes['story_encoding_mlp_dropout'] = Dropout(p)(nodes['story_encoding_mlp'])
nodes['answer_plus_question_mlp_dropout'] = Dropout(p)(nodes['answer_plus_question_mlp'])
# norm
unit_layer = UnitNormalization()
nodes['story_encoding_mlp_dropout_norm'] = unit_layer(nodes['story_encoding_mlp_dropout'])
nodes['answer_plus_question_norm'] = unit_layer(nodes['answer_plus_question_mlp_dropout'])
# cosine
nodes['story_dot_answer'] = merge([nodes['story_encoding_mlp_dropout_norm'],
nodes['answer_plus_question_norm']],
mode='dot', dot_axes=[2, 2])
# WORD LEVEL
# story mlps for word score and distance score
trainable_word_mlp = self.model_config['PHM']['trainable_word_mlp']
if trainable_word_mlp:
story_word_dense = NTimeDistributed(
Dense(D, init="identity", activation=activation, W_regularizer=l2(mlp_l2),
trainable=trainable_word_mlp), first_n=3)
# q mlps for word and distance scores
q_or_a_word_dense = NTimeDistributed(
Dense(D, init="identity", activation=activation, W_regularizer=l2(mlp_l2),
trainable=trainable_word_mlp), first_n=3)
else:
linear_activation = Activation('linear')
story_word_dense = linear_activation
q_or_a_word_dense = linear_activation
ninputs, noutputs = [], []
tpls = [(True, 'story_word_embedding1', 'story_word_mlp'),
('use_slide_window_inside_sentence', 'reordered_story_word_embedding', 'reordered_story_word_mlp'),
('use_slide_window_word', 'story_attentive_word_embedding', 'story_attentive_word_embedding_mlp'),
('use_slide_window_reordered_word', 'reordered_story_attentive_word_embedding', 'reordered_story_attentive_word_embedding_mlp')
]
for tpl in tpls:
a, b, c = tpl
if a is True or config[a]:
ninputs.append(b)
noutputs.append(c)
if b in ['reordered_story_word_embedding', 'story_word_embedding1']:
for ngram in config['ngram_inputs']:
ninputs.append('%s_%sgram' % (b, ngram))
noutputs.append('%s_%sgram' % (c, ngram))
for input, output in zip(ninputs, noutputs):
nodes[output] = story_word_dense(self._get_node(input))
inputs = ['question_word_embedding', 'answer_word_embedding', 'qa_word_embedding']
outputs = ['question_word_mlp', 'answer_word_mlp', 'qa_word_mlp']
for input, output in zip(inputs, outputs):
nodes[output] = q_or_a_word_dense(self._get_node(input))
# SIMILARITY MATRICES
# first for word scores
# cosine similarity matrix based on sentence and q
nodes['sim_matrix_q'] = WordByWordMatrix(is_q=True)([nodes['story_word_mlp'], nodes['question_word_mlp']])
# cosine similarity matrix based on sentence and a
nodes['sim_matrix_a'] = WordByWordMatrix()([nodes['story_word_mlp'], nodes['answer_word_mlp']])
# WORD-BY-WORD SCORES
# q
nodes['s_q_wbw_score'] = WordByWordScores(trainable=False, is_q=True, alpha=1., threshold=0.15,
wordbyword_merge_type=config['wordbyword_merge_type'],
)([nodes['sim_matrix_q'], nodes['__w_question_wbw']])
# a
nodes['s_a_wbw_score'] = WordByWordScores(trainable=False, alpha=1., threshold=0.15,
wordbyword_merge_type=config['wordbyword_merge_type'], )(
[nodes['sim_matrix_a'], nodes['__w_answer_wbw']])
# mean
nodes['story_dot_answer_words'] = GeneralizedMean(mean_type=config['mean_type'],
trainable=config['trainable_story_dot_answer_words']) \
([nodes['s_q_wbw_score'], nodes['s_a_wbw_score']])
# SLIDING WINDOW INSIDE SENTENCE
if config['use_slide_window_inside_sentence']:
# q+a mlp for word score
# construct cosine similarity matrix based on sentence and qa, for word score
_inputs = [nodes['reordered_story_word_mlp'], nodes['qa_word_mlp']]
nodes['wordbyword_slide_sum_within_sentence'] = \
WordByWordSlideSumInsideSentence(len(_inputs),
window_size=config['window_size_word_inside'],
alpha=config['alpha_slide_window_word_inside'],
use_gaussian_window=config['use_gaussian_window_word_inside'],
gaussian_std=config['gaussian_sd_word_inside'],
trainable=config['trainable_slide_window_word_inside'])(_inputs)
# COMBINE LEVELS
# sum word-based and sentence-based similarity scores
inputs = ['story_dot_answer_words', 'story_dot_answer']
if config['use_slide_window_sentence']:
inputs.append('story_dot_answer_slide')
nodes["story_dot_answer_slide"] = SlideSum(alpha=config['alpha_slide_window'],
use_gaussian_window=config['use_gaussian_window'],
trainable=config['trainable_slide_window'])(
nodes['story_dot_answer'])
if config['use_slide_window_inside_sentence']:
inputs.append('wordbyword_slide_sum_within_sentence')
if self.model_config['PHM']['use_depend_score']:
# SENTENCE-QA DEPENDENCY LEVEL
inputs.append('lcc_score_matrix')
nodes['lcc_score_matrix'] = DependencyDistanceScore(config['alpha_depend_score'])(
self._get_node('input_dep'))
# sum scores from different component of the model on sentence level.
# sentence level score merge
layers_s_input = [nodes[x] for x in inputs]
weights_s = [1.] * len(layers_s_input)
nodes['word_plus_sent_sim'] = Combination(len(layers_s_input), input_dim=3, weights=weights_s,
combination_type=config['sentence_ensemble'],
trainable=config['trainable_sentence_ensemble'])(layers_s_input)
# extract max over sentences
nodes['story_dot_answer_max'] = TimeDistributedMerge(mode='max', axis=1)(nodes['word_plus_sent_sim'])
# word sliding window
word_sliding_window_output = ['story_dot_answer_max']
if config['use_slide_window_word']:
# q+a mlp for word score
# construct cosine similarity matrix based on sentence and qa, for word score
temp_inputs = [nodes['story_attentive_word_embedding_mlp'], nodes['qa_word_mlp']]
if config['use_qa_idf']:
temp_inputs.append(nodes['__w_question_answer'])
nodes['wordbyword_slide_sum'] = WordByWordSlideSum(len(temp_inputs),
window_size=config['window_size_word'],
alpha=config['alpha_slide_window_word'],
use_gaussian_window=config['use_gaussian_window_word'],
gaussian_std=config['gaussian_sd_word'],
trainable=config['trainable_slide_window_word'])(
temp_inputs)
word_sliding_window_output.append('wordbyword_slide_sum')
if config['use_slide_window_reordered_word']:
# q+a mlp for word score
# construct cosine similarity matrix based on sentence and qa, for word score
temp_inputs = [nodes['reordered_story_attentive_word_embedding_mlp'], nodes['qa_word_mlp']]
if config['use_qa_idf']:
temp_inputs.append(nodes['__w_question_answer'])
nodes['reordered_wordbyword_slide_sum'] = WordByWordSlideSum(len(temp_inputs),
window_size=config[
'window_size_reordered_word'],
alpha=config[
'alpha_slide_window_reordered_word'],
use_gaussian_window=config[
'use_gaussian_window_reordered_word'],
gaussian_std=config[
'gaussian_sd_reordered_word'],
trainable=config[
'trainable_slide_window_reordered_word'])(
temp_inputs
)
word_sliding_window_output.append('reordered_wordbyword_slide_sum')
# Extract top_n sentence for each answer
if config['top_n_wordbyword']:
layers_name = ['word_plus_sent_sim', 'story_word_embedding1', 'qa_word_embedding', '__w_question_answer']
layers = [nodes[x] for x in layers_name]
top_n_name = 'top_n_wordbyword'
nodes[top_n_name] = TopNWordByWord(top_n=config['top_n'], nodes=nodes, use_sum=config['top_n_use_sum'],
trainable=True)(layers)
word_sliding_window_output.append(top_n_name)
ngram_output = [self._add_ngram_network(ngram, story_encoding_mlp) for ngram in config['ngram_inputs']]
# final score merge
layers_input = [nodes[x] for x in word_sliding_window_output + ngram_output]
weights = [1.] * len(layers_input)
for i in range(len(ngram_output)):
weights[-i - 1] = 1.
"""
# also aggregate scores that were already aggregated on sentence level.
sentence_level_weight = 0.1
for layer_name in sentence_level_merge_layers:
layer_max = layer_name + "_max"
if layer_max not in nodes:
add_node(TimeDistributedMergeEnhanced(mode='max'), layer_max, input=layer_name)
layers_input.append(nodes[layer_max])
weights.append(sentence_level_weight)"""
nodes['story_dot_answer_combined_max'] = Combination(len(layers_input), weights=weights,
combination_type=config['answer_ensemble'],
trainable=config['trainable_answer_ensemble'])(
layers_input)
# apply not-switch
input_mul = self._get_node('input_negation_questions')
nodes['story_dot_answer_max_switch'] = merge([nodes['story_dot_answer_combined_max'], input_mul], mode='mul')
activation_final = Activation('linear', name='y_hat') \
if self.model_config['optimizer']['loss'] == 'ranking_loss' else Activation(
'softmax', name='y_hat')
prediction = activation_final(nodes['story_dot_answer_max_switch'])
inputs = self.inputs_nodes.values()
model = Model(input=inputs, output=prediction)
optimizer = self._get_optimizer()
model.compile(loss=self._get_loss_dict(), optimizer=optimizer, metrics={'y_hat': 'accuracy'})
self.graph = model
def create_model(self, embedding_dimensions, lstm_dimensions, dense_dimensions, optimizer, embeddings=None,
embeddings_trainable=True):
"""
creates the neural network model, optionally using precomputed embeddings applied to the training data
:return:
"""
num_words = len(self.tokenizer.word_index)
logger.info('Creating a model based on %s unique tokens.', num_words)
# create the shared embedding layer (with or without pre-trained weights)
embedding_shared = None
if embeddings is None:
embedding_shared = Embedding(num_words + 1, embedding_dimensions, input_length=None, mask_zero=True,
trainable=embeddings_trainable, name="embedding_shared")
else:
logger.info('Importing pre-trained word embeddings.')
embeddings_index = load_embeddings(embeddings)
# indices in word_index start with a 1, 0 is reserved for masking padded value
embedding_matrix = np.zeros((num_words + 1, embedding_dimensions))
for word, i in self.tokenizer.word_index.items():
embedding_vector = embeddings_index.get(word)
if embedding_vector is not None:
# words not found in embedding index will be all-zeros.
embedding_matrix[i] = embedding_vector
else:
logger.warning('Word not found in embeddings: %s', word)
embedding_shared = Embedding(num_words + 1, embedding_dimensions, input_length=None, mask_zero=True,
trainable=embeddings_trainable, weights=[embedding_matrix],
name="embedding_shared")
input_state = Input(batch_shape=(None, None), name="input_state")
input_action = Input(batch_shape=(None, None), name="input_action")
embedding_state = embedding_shared(input_state)
embedding_action = embedding_shared(input_action)
lstm_shared = LSTM(lstm_dimensions, name="lstm_shared")
lstm_state = lstm_shared(embedding_state)
lstm_action = lstm_shared(embedding_action)
dense_state = Dense(dense_dimensions, activation='tanh', name="dense_state")(lstm_state)
dense_action = Dense(dense_dimensions, activation='tanh', name="dense_action")(lstm_action)
model_state = Model(inputs=input_state, outputs=dense_state, name="state")
model_action = Model(inputs=input_action, outputs=dense_action, name="action")
self.model_state = model_state
self.model_action = model_action
input_dot_state = Input(shape=(dense_dimensions,))
input_dot_action = Input(shape=(dense_dimensions,))
dot_state_action = Dot(axes=-1, normalize=True, name="dot_state_action")([input_dot_state, input_dot_action])
model_dot_state_action = Model(inputs=[input_dot_state, input_dot_action], outputs=dot_state_action,
name="dot_state_action")
self.model_dot_state_action = model_dot_state_action
model = Model(inputs=[model_state.input, model_action.input],
outputs=model_dot_state_action([model_state.output, model_action.output]),
name="model")
model.compile(optimizer=optimizer, loss='mse')
self.model = model
print('---------------')
print('Complete model:')
model.summary()
print('---------------')
def rpn_initialize(options):
config_output_filename = options.config_filename
with open(config_output_filename, 'rb') as f_in:
c = pickle.load(f_in)
import nn_cnn_3_layer as nn
# turn off any data augmentation at test time
c.use_horizontal_flips = False
c.use_vertical_flips = False
c.rot_90 = False
img_list_path = options.test_path
class_mapping = c.class_mapping
if 'bg' not in class_mapping:
class_mapping['bg'] = len(class_mapping)
class_mapping = {v: k for k, v in class_mapping.items()}
print(class_mapping)
class_to_color = {class_mapping[v]: np.random.randint(0, 255, 3) for v in class_mapping}
c.num_rois = int(options.num_rois)
# if c.network == 'resnet50':
# num_features = 1024
# elif c.network == 'vgg':
# num_features = 512
input_shape_img = (None, None, 3)
# input_shape_features = (None, None, num_features)
img_input = Input(shape=input_shape_img)
# roi_input = Input(shape=(c.num_rois, 4))
# feature_map_input = Input(shape=input_shape_features)
# define the base network
shared_layers = nn.nn_base(img_input, trainable=True)
# define the RPN, built on the base layers
num_anchors = len(c.anchor_box_scales) * len(c.anchor_box_ratios)
rpn_layers = nn.rpn(shared_layers, num_anchors)
# classifier = nn.classifier(feature_map_input, roi_input, c.num_rois, nb_classes=len(class_mapping), trainable=True)
model_rpn = Model(img_input, rpn_layers)
# model_classifier_only = Model([feature_map_input, roi_input], classifier)
# model_classifier = Model([feature_map_input, roi_input], classifier)
print('Loading weights from {}'.format(options.rpn_weight_path))
model_rpn.load_weights(options.rpn_weight_path, by_name=True)
# model_classifier.load_weights(c.model_path, by_name=True)
model_rpn.compile(optimizer='sgd', loss='mse')
# model_classifier.compile(optimizer='sgd', loss='mse')
model_rpn.summary()
model_classifier = load_model(options.classify_model_path)
model_classifier.summary()
all_imgs = []
classes = {}
bbox_threshold = 0.8
visualise = True
return c, model_rpn, model_classifier
def unet_model_3d(first_input_shape, second_input_shape, nb_classes, feature_size):
channel_first_first_input = Input(first_input_shape)
first_input = Permute([2,3,4,1])(channel_first_first_input)
first_conv_permute = Permute([4,2,3,1])(first_input)
first_gpooling_0 = GlobalAveragePooling3D()(first_conv_permute)
first_gpooling_dense_0 = Dense(units = 32, activation='linear')(first_gpooling_0)
first_gpooling_dense_1_1 = Dense(units = 29, activation='sigmoid')(first_gpooling_dense_0)
first_gpooling_fused_2 = Lambda(fuse)([first_conv_permute,first_gpooling_dense_1_1])
first_conv_layer0 = Conv3D(8, (5, 5, 5), padding = 'same', activation='linear')(first_input)
first_conv_permute = Permute([4,2,3,1])(first_conv_layer0)
first_gpooling_0 = GlobalAveragePooling3D()(first_conv_permute)
first_gpooling_dense_0 = Dense(units = 32, activation='linear')(first_gpooling_0)
first_gpooling_dense_1_0 = Dense(units = 29, activation='sigmoid')(first_gpooling_dense_0)
first_gpooling_fused_0 = Lambda(fuse)([first_conv_permute,first_gpooling_dense_1_0])
first_conv_layer1 = Conv3D(8, (3, 3, 3), padding = 'same', activation='linear')(first_conv_layer0)
first_conv_permute = Permute([4,2,3,1])(first_conv_layer1)
first_gpooling_0 = GlobalAveragePooling3D()(first_conv_permute)
first_gpooling_dense_0 = Dense(units = 32, activation='linear')(first_gpooling_0)
first_gpooling_dense_1_1 = Dense(units = 29, activation='sigmoid')(first_gpooling_dense_0)
first_gpooling_fused_1 = Lambda(fuse)([first_conv_permute,first_gpooling_dense_1_1])
first_gpooling_add_0 = Add()([first_gpooling_fused_0, first_gpooling_fused_1,first_gpooling_fused_2])
first_conv_layer2 = Conv2D(16, (3, 3), padding = 'same', activation='linear')(first_gpooling_add_0)
first_pooling_layer1 = MaxPooling2D(pool_size=(2, 2))(first_conv_layer2)
first_conv_layer3 = Conv2D(16, (3, 3), padding = 'same', activation='linear')(first_pooling_layer1)
first_pooling_layer2 = MaxPooling2D(pool_size=(2, 2))(first_conv_layer3)
first_conv_layer4 = Conv2D(16, (3, 3), padding = 'same', activation='linear')(first_pooling_layer2)
first_pooling_layer3 = MaxPooling2D(pool_size=(2, 2),padding='same')(first_conv_layer4)
first_flatten_layer1 = Flatten()(first_pooling_layer3)
first_dense_layer1 = Dense(units = feature_size, activation='relu')(first_flatten_layer1)
first_dense_layer2 = Dense(units=feature_size, activation='relu')(first_dense_layer1)
base_model = ResNet50(weights='imagenet',include_top=False,input_shape=[128,128,3])
second_input = base_model.input
resnet50_activation_98_output = base_model.output
resnet50_gpooling = GlobalAveragePooling2D()(resnet50_activation_98_output)
concat_layer = concatenate([first_dense_layer2, resnet50_gpooling],axis = 1)
input_target = Input(shape=(1,))
centers = Embedding(nb_classes, feature_size*3)(input_target)
l2_loss = Lambda(center_loss, name='l2_loss')([concat_layer, centers])
concat_result = Dense(units = nb_classes, activation = 'softmax',name = 'softmax')(concat_layer)
concat_model = Model(inputs=[channel_first_first_input,second_input,input_target], outputs = [concat_result,l2_loss])
concat_test_model = Model(inputs=[channel_first_first_input, second_input], outputs=concat_result)
# return model_train, model_test, second_train_model
return concat_model,concat_test_model
class RM(BaseModel):
def __init__(self, max_len=125, class_num=9, use_development_set=True):
super(RM, self).__init__(use_development_set)
self.max_len = max_len
self.class_num = class_num
self.name = "mask_attention"
def build_model(self):
sentence = Concatenate()([
self.sen_embedding,
# self.sen_entity_type_embedding,
self.position_t_embedding,
self.position_a_embedding
])
sentence = Bidirectional(
GRU(300,
activation="relu",
return_sequences=True,
recurrent_dropout=0.3,
dropout=0.3))(sentence)
average_layer = Lambda(average, output_shape=no_change)
position_mt = average_layer(self.position_mt)
position_ma = average_layer(self.position_ma)
trigger = Dot(axes=[1, 1])([sentence, position_mt]) # (?, 600)
entity = Dot(axes=[1, 1])([sentence, position_ma]) # (?, 600)
attention = Dense(1, activation='tanh')(sentence) # (?, 125, 1)
attention = Lambda(lambda x: K.softmax(K.squeeze(x, axis=2)),
output_shape=output_shape2)(attention) # (?, 125)
weighted_sentence = Dot(axes=[1, 1])([sentence, attention])
x_layer = Lambda(
lambda x: K.reshape(x, [-1, self.TRIGGER_TYPE_VEC_DIM]),
output_shape=output_shape)
trigger_type = x_layer(self.trigger_type_embedding) # (?, 50)
entity_type = x_layer(self.entity_type_embedding) # (?, 50)
x = Concatenate()(
[trigger_type, entity_type, trigger, entity,
weighted_sentence]) # (?, 1300)
x = Dropout(rate=0.5)(x)
output = Dense(9, activation='softmax')(x)
return output
def train_model(self, max_epoch=30):
evaluator = Evaluator(true_labels=self.test_labels,
sentences=self.test_sentence_words_input,
position_mt=self.test_position_mt,
position_me=self.test_position_ma,
correction_factor=self.correction_factor)
log = open("../log/" + self.name + ".txt", 'a+', encoding='utf-8')
for i in range(max_epoch):
self.model.fit(
{
'sentence_word': self.train_sentence_words_input,
# 'sentence_entity_type': self.train_sentence_entity_inputs,
'position_t': self.train_position_t,
'position_a': self.train_position_a,
'trigger_type': self.train_trigger_type,
'entity_type': self.train_entity_type,
'trigger_mask': self.train_position_mt,
'entity_mask': self.train_position_ma
},
self.train_labels,
epochs=1,
batch_size=256,
verbose=1)
print("# -- test set --- #")
results = self.model.predict(
{
'sentence_word': self.test_sentence_words_input,
# 'sentence_entity_type': self.test_sentence_entity_inputs,
'position_t': self.test_position_t,
'position_a': self.test_position_a,
'trigger_type': self.test_trigger_type,
'entity_type': self.test_entity_type,
'trigger_mask': self.test_position_mt,
'entity_mask': self.test_position_ma
},
batch_size=128,
verbose=0)
print("--------------epoch " + str(i + 1) +
" ---------------------")
macro_f1, micro_F1, p, r = evaluator.get_f1(predictions=results,
epoch=i + 1)
log.write("epoch: " + str(i + 1) + " " + str(p) + " " + str(r) +
" " + str(micro_F1) + "\n")
if (i + 1) % 5 == 0:
print("current max macro_F1 score: " +
str(evaluator.max_macro_F1 * 100))
print("max macro_F1 is gained in epoch " +
str(evaluator.max_macro_F1_epoch))
print("current max micro_F1 score: " +
str(evaluator.max_micro_F1 * 100))
print("max micro_F1 is gained in epoch " +
str(evaluator.max_micro_F1_epoch))
log.write("current max macro_F1 score: " +
str(evaluator.max_macro_F1 * 100) + "\n")
log.write("max macro_F1 is gained in epoch " +
str(evaluator.max_macro_F1_epoch) + "\n")
log.write("current max micro_F1 score: " +
str(evaluator.max_micro_F1 * 100) + "\n")
log.write("max micro_F1 is gained in epoch " +
str(evaluator.max_micro_F1_epoch) + "\n")
print(
"------------------------------------------------------------")
log.close()
def make_input(self):
inputs = [None] * 7
inputs[0] = Input(shape=(self.max_len, ),
dtype='int32',
name='sentence_word')
# inputs[1] = Input(shape=(self.max_len,), dtype='int32', name='sentence_entity_type')
inputs[1] = Input(shape=(self.max_len, ),
dtype='int32',
name='position_t')
inputs[2] = Input(shape=(self.max_len, ),
dtype='int32',
name='position_a')
inputs[3] = Input(shape=(1, ), dtype='int32', name='trigger_type')
inputs[4] = Input(shape=(1, ), dtype='int32', name='entity_type')
inputs[5] = Input(shape=(self.max_len, ),
dtype='float32',
name='trigger_mask')
inputs[6] = Input(shape=(self.max_len, ),
dtype='float32',
name='entity_mask')
return inputs
def compile_model(self):
inputs = [
self.sen_input, self.position_t, self.position_a,
self.trigger_type_input, self.entity_type_input, self.position_mt,
self.position_ma
] = self.make_input()
[
self.sen_embedding, self.position_t_embedding,
self.position_a_embedding, self.trigger_type_embedding,
self.entity_type_embedding
] = self.embedded()
self.output = self.build_model()
self.model = Model(inputs=inputs, outputs=self.output)
self.model.compile(optimizer='adam',
loss='categorical_crossentropy',
metrics=['acc'])
print(self.model.summary())
def embedded(self):
self.sentence_embedding_layer = Embedding(
self.num_words + 2,
self.EMBEDDING_DIM,
weights=[self.embedding_matrix],
input_length=self.max_len,
trainable=False,
mask_zero=True)
sentence_embedding = self.sentence_embedding_layer(self.sen_input)
position_t_embedding_layer = Embedding(125,
self.POSITION_VEC_DIM,
input_length=self.max_len,
trainable=True,
mask_zero=False)
position_t_embedding = position_t_embedding_layer(self.position_t)
position_a_embedding_layer = Embedding(125,
self.POSITION_VEC_DIM,
input_length=self.max_len,
trainable=True,
mask_zero=False)
position_a_embedding = position_a_embedding_layer(self.position_a)
trigger_type_embedding_layer = Embedding(38,
self.TRIGGER_TYPE_VEC_DIM,
input_length=1,
trainable=True,
mask_zero=False)
trigger_type_embedding = trigger_type_embedding_layer(
self.trigger_type_input)
entity_type_embedding = trigger_type_embedding_layer(
self.entity_type_input)
return [
sentence_embedding, position_t_embedding, position_a_embedding,
trigger_type_embedding, entity_type_embedding
]
def unet_model_3d(input_shape,
pool_size=(2, 2, 2),
n_labels=n_labels,
deconvolution=False,
depth=3,
n_base_filters=32,
include_label_wise_dice_coefficients=False,
batch_normalization=True,
activation_name="sigmoid"):
"""
Builds the 3D UNet Keras model.f
:param metrics: List metrics to be calculated during model training (default is dice coefficient).
:param include_label_wise_dice_coefficients: If True and n_labels is greater than 1, model will report the dice
coefficient for each label as metric.
:param n_base_filters: The number of filters that the first layer in the convolution network will have. Following
layers will contain a multiple of this number. Lowering this number will likely reduce the amount of memory required
to train the model.
:param depth: indicates the depth of the U-shape for the model. The greater the depth, the more max pooling
layers will be added to the model. Lowering the depth may reduce the amount of memory required for training.
:param input_shape: Shape of the input data (n_chanels, x_size, y_size, z_size). The x, y, and z sizes must be
divisible by the pool size to the power of the depth of the UNet, that is pool_size^depth.
:param pool_size: Pool size for the max pooling operations.
:param n_labels: Number of binary labels that the model is learning.
:param initial_learning_rate: Initial learning rate for the model. This will be decayed during training.
:param deconvolution: If set to True, will use transpose convolution(deconvolution) instead of up-sampling. This
increases the amount memory required during training.
:return: Untrained 3D UNet Model
"""
inputs = Input(input_shape)
# set image specifics
kernel = (3, 3, 3) # kernel size
s = 2 # stride
#img_height, img_width = img_size[0], img_size[1]
padding = 'same'
conv1 = create_convolution_block(
input_layer=inputs,
n_filters=n_base_filters * 4, # 256 * 256 *8
batch_normalization=batch_normalization)
conv1 = create_convolution_block(input_layer=conv1,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
pool1 = Conv3D(n_base_filters, (3, 3, 3),
padding=padding,
strides=(2, 2, 1))(conv1)
conv2 = create_convolution_block(
input_layer=pool1,
n_filters=n_base_filters * 4, # 128 * 128 *8
batch_normalization=batch_normalization)
conv2 = create_convolution_block(input_layer=conv2,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
pool2 = Conv3D(n_base_filters * 2, (3, 3, 3),
padding=padding,
strides=(1, 1, 2))(conv2)
conv3 = create_convolution_block(
input_layer=pool2,
n_filters=n_base_filters * 2, # 128 * 128 *4
batch_normalization=batch_normalization)
conv3 = create_convolution_block(input_layer=conv3,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
pool3 = Conv3D(n_base_filters * 4, (3, 3, 3),
padding=padding,
strides=(2, 2, 1))(conv3)
conv4 = create_convolution_block(
input_layer=pool3,
n_filters=n_base_filters * 2, # 64 * 64 *4
batch_normalization=batch_normalization)
conv4 = create_convolution_block(input_layer=conv4,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
pool4 = Conv3D(n_base_filters * 2, (3, 3, 3),
padding=padding,
strides=(2, 2, 1))(conv4)
conv5 = create_convolution_block(
input_layer=pool4,
n_filters=n_base_filters, # 32 * 32 *4
batch_normalization=batch_normalization)
conv5 = create_convolution_block(input_layer=conv5,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
pool5 = Conv3D(n_base_filters * 4, (3, 3, 3),
padding=padding,
strides=(2, 2, 2))(conv5)
conv6 = create_convolution_block(
input_layer=pool5,
n_filters=n_base_filters * 2, # 16 * 16 *2
batch_normalization=batch_normalization)
conv6 = create_convolution_block(input_layer=conv6,
n_filters=n_base_filters * 2,
batch_normalization=batch_normalization)
convskip0 = Conv3D(n_base_filters * 8, (1, 1, 1),
padding=padding,
strides=(1, 1, 1))(inputs)
convskip0 = BatchNormalization(axis=-1)(convskip0)
convskip0 = Activation('relu')(convskip0)
convskip0 = Conv3D(n_base_filters * 4, (2, 2, 1),
padding=padding,
strides=(1, 1, 1))(convskip0)
convskip0 = BatchNormalization(axis=-1)(convskip0)
convskip0 = Activation('relu')(convskip0)
convskip0 = Conv3D(n_base_filters * 4, (2, 2, 1),
padding=padding,
strides=(1, 1, 1))(convskip0)
convskip0 = BatchNormalization(axis=-1)(convskip0)
convskip0 = Activation('relu')(convskip0)
convskip0 = Conv3D(n_base_filters * 4, (1, 1, 2),
padding=padding,
strides=(1, 1, 1))(convskip0)
convskip0 = BatchNormalization(axis=-1)(convskip0)
convskip0 = Activation('relu')(convskip0)
convskip1 = Conv3D(n_base_filters * 4, (1, 1, 1),
padding=padding,
strides=(1, 1, 1))(conv1)
convskip1 = BatchNormalization(axis=-1)(convskip1)
convskip1 = Activation('relu')(convskip1)
convskip1 = Conv3D(n_base_filters * 4, (1, 1, 2),
padding=padding,
strides=(1, 1, 1))(convskip1)
convskip1 = BatchNormalization(axis=-1)(convskip1)
convskip1 = Activation('relu')(convskip1)
convskip1 = Conv3D(n_base_filters * 4, (1, 1, 1),
padding=padding,
strides=(1, 1, 1))(convskip1)
convskip1 = BatchNormalization(axis=-1)(convskip1)
convskip1 = Activation('relu')(convskip1)
convskip1 = Conv3D(n_base_filters * 4, (1, 1, 2),
padding=padding,
strides=(1, 1, 1))(convskip1)
convskip1 = BatchNormalization(axis=-1)(convskip1)
convskip1 = Activation('relu')(convskip1)
convskip2 = Conv3D(n_base_filters * 2, (1, 1, 1),
padding=padding,
strides=(1, 1, 1))(conv2)
convskip2 = BatchNormalization(axis=-1)(convskip2)
convskip2 = Activation('relu')(convskip2)
convskip2 = Conv3D(n_base_filters * 2, (1, 1, 2),
padding=padding,
strides=(1, 1, 1))(convskip2)
convskip2 = BatchNormalization(axis=-1)(convskip2)
convskip2 = Activation('relu')(convskip2)
convskip2 = Conv3D(n_base_filters * 2, (1, 1, 1),
padding=padding,
strides=(1, 1, 1))(convskip2)
convskip2 = BatchNormalization(axis=-1)(convskip2)
convskip2 = Activation('relu')(convskip2)
convskip2 = Conv3D(n_base_filters * 2, (1, 1, 2),
padding=padding,
strides=(1, 1, 1))(convskip2)
convskip2 = BatchNormalization(axis=-1)(convskip2)
convskip2 = Activation('relu')(convskip2)
up_convolution7 = UpSampling3D(size=(2, 2, 2))(conv6) # 32 * 32 *4
concat7 = concatenate([up_convolution7, conv5], axis=-1)
conv7 = create_convolution_block(input_layer=concat7,
n_filters=n_base_filters * 2,
batch_normalization=batch_normalization)
conv7 = create_convolution_block(input_layer=conv7,
n_filters=n_base_filters * 2,
batch_normalization=batch_normalization)
up_convolution8 = UpSampling3D(size=(2, 2, 1))(conv7) # 64 * 64 *4
concat8 = concatenate([up_convolution8, conv4], axis=-1)
conv8 = create_convolution_block(input_layer=concat8,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
conv8 = create_convolution_block(input_layer=conv8,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
up_convolution8 = UpSampling3D(size=(2, 2, 1))(conv8) # 128 * 128 *4
concat9 = concatenate([up_convolution8, conv3], axis=-1)
conv9 = create_convolution_block(input_layer=concat9,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
conv9 = create_convolution_block(input_layer=conv9,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
up_convolution10 = UpSampling3D(size=(1, 1, 2))(conv9) # 128 * 128 *8
concat10 = concatenate([up_convolution10, conv2, convskip2], axis=-1)
conv10 = create_convolution_block(input_layer=concat10,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
conv10 = create_convolution_block(input_layer=conv10,
n_filters=n_base_filters,
batch_normalization=batch_normalization)
up_convolution11 = UpSampling3D(size=(2, 2, 1))(conv10) # 256*256 *8
concat11 = concatenate([up_convolution11, conv1, convskip0], axis=-1)
conv11 = create_convolution_block(input_layer=concat11,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
conv11 = create_convolution_block(input_layer=conv11,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
concat12 = concatenate([conv11, convskip1], axis=-1)
concat12 = create_convolution_block(
input_layer=conv11,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
concat12 = create_convolution_block(
input_layer=concat12,
n_filters=n_base_filters * 4,
batch_normalization=batch_normalization)
final_convolution = Conv3D(n_labels, (1, 1, 1))(conv11)
act = Activation(activation_name)(final_convolution)
model = Model(inputs=inputs, outputs=act)
return model
