def get_callbacks(use_early_stopping=True, use_reduce_lr=True):
callback_list = []
if (use_early_stopping):
callback_list.append(
callbacks.EarlyStopping(monitor='val_loss',
min_delta=0,
patience=10,
verbose=keras_verbosity,
mode='auto'))
if (use_reduce_lr):
callback_list.append(
callbacks.ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=5,
verbose=keras_verbosity,
mode='auto',
epsilon=0.0001,
cooldown=0,
min_lr=0))
return callback_list
def train_model(model_name,weights_save_path):
with h5py.File(hdf5_path + mode_list[0] + "_2D_data_" + str(index) + ".h5", "r") as f:
train_img = f["batch_patches"].value[..., 0:6] # (num,patch_h,patch_w,6)
train_gt = f["batch_patches"].value[..., 6] # (num,patch_h,patch_w)
with h5py.File(hdf5_path + mode_list[1] + "_2D_data_" + str(index) + ".h5", "r") as f:
val_img = f["batch_patches"].value[..., 0:6] # (num,patch_h,patch_w,6)
val_gt = f["batch_patches"].value[..., 6] # (num,patch_h,patch_w)
print(train_img.shape)
if model_name == "Unet":
model = unet.unet(input_height=patch_h, input_width=patch_w)
elif model_name == "Nonlocal dsv Unet":
model = unet_nonlocal.unet_nonlocal(input_height=patch_h, input_width=patch_w)
else:
model = unet_nonlocal.res_unet_nonlocal(input_height=patch_h, input_width=patch_w)
cp = [callbacks.EarlyStopping(monitor='val_dice',
patience=10,
mode='max'),
callbacks.ModelCheckpoint(filepath=weights_save_path,
monitor='val_dice',
save_best_only=True,
save_weights_only=True,
mode='max',
verbose=1)]
print("Training " + model_name + " Model")
if load_weights == True:
print("Loading " + model_name + " Model Weights")
model.load_weights(weights_save_path)
history = model.fit(train_img, train_gt[..., None], batch_size=batch_size, epochs=epochs,
validation_data=(val_img, val_gt[..., None]),
shuffle=True, callbacks=cp)
eval_metrics = model.evaluate(val_img, val_gt[..., None])
visualize_loss(history)
return eval_metrics
def dense_train(space):
''' train lightgbm booster based on training / validaton set -> give predictions of Y '''
params = space.copy()
input_shape = (X_train.shape[-1], ) # input shape depends on x_fields used
input_img = Input(shape=input_shape)
init_nodes = params['init_nodes'] # fisrt dense layer - number of nodes
nodes_mult = params['nodes_mult'] # nodes growth rate
mult_freq = params['mult_freq'] # grow every X layer
mult_start = params['mult_start'] # grow from X layer
end_nodes = params['end_nodes'] # maximum number of nodes
if params['num_Dense_layer'] < 4:
params['init_nodes'] = init_nodes = 16
d_1 = Dense(init_nodes, activation=params['activation'])(
input_img) # remove kernel_regularizer=regularizers.l1(params['l1'])
d_1 = Dropout(params['dropout'])(d_1)
for i in range(1, params['num_Dense_layer']):
temp_nodes = int(
min(
init_nodes * (2**(nodes_mult * max(
(i - mult_start + 3) // mult_freq, 0))), end_nodes))
d_1 = Dense(temp_nodes, activation=params['activation'])(d_1)
if i != params[
'num_Dense_layer'] - 1: # last dense layer has no dropout
d_1 = Dropout(params['dropout'])(d_1)
f_x = Dense(1)(d_1)
callbacks_list = [
callbacks.ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=10),
callbacks.EarlyStopping(monitor='val_loss', patience=10, mode='auto')
] # add callbacks
lr_val = 10**-int(params['learning_rate'])
adam = optimizers.Adam(lr=lr_val)
model = Model(input_img, f_x)
model.compile(adam, loss='mae')
model.summary()
history = model.fit(X_train,
Y_train,
epochs=50,
batch_size=params['batch_size'],
validation_data=(X_valid, Y_valid),
callbacks=callbacks_list,
verbose=1)
Y_test_pred = model.predict(X_test)
Y_train_pred = model.predict(X_train)
Y_valid_pred = model.predict(X_valid)
return Y_test_pred, Y_train_pred, Y_valid_pred, history
def test_validate_callbacks_predefined_callbacks(self):
supported_predefined_callbacks = [
callbacks.TensorBoard(),
callbacks.CSVLogger(filename='./log.csv'),
callbacks.EarlyStopping(),
callbacks.ModelCheckpoint(filepath='./checkpoint'),
callbacks.TerminateOnNaN(),
callbacks.ProgbarLogger(),
callbacks.History(),
callbacks.RemoteMonitor()
]
distributed_training_utils.validate_callbacks(
supported_predefined_callbacks, adam.Adam())
unsupported_predefined_callbacks = [
callbacks.ReduceLROnPlateau(),
callbacks.LearningRateScheduler(schedule=lambda epoch: 0.001)
]
for callback in unsupported_predefined_callbacks:
with self.assertRaisesRegex(ValueError,
'You must specify a Keras Optimizer V2'):
distributed_training_utils.validate_callbacks([callback],
v1_adam.AdamOptimizer())
def define_callbacks(output, batch_size):
csv_logger = callbacks.CSVLogger(join(output, 'training.log'))
earlystop = callbacks.EarlyStopping(monitor='val_loss', patience=2)
tensorboard = callbacks.TensorBoard(batch_size=batch_size)
fpath = join(
output,
'weights.{epoch:02d}-{loss:.2f}-{acc:.2f}-{val_loss:.2f}-{val_acc:.2f}.hdf5'
)
cp_cb = callbacks.ModelCheckpoint(filepath=fpath,
monitor='val_loss',
save_best_only=True)
return [csv_logger, earlystop, tensorboard, cp_cb]
def _create_validation_early_stopping(
cfg_services: dict) -> callbacks.EarlyStopping:
"""Create an early stopping callback that monitors a validation 'metric'.
Args:
cfg_services: dict, services subsection of config.
Returns:
EarlyStopping, EarlyStopping callback that monitors a validation 'metric'.
"""
early_stopping_params = cfg_services["validation_early_stopping"]
early_stopping_params["monitor"] = _force_monitor_to_mode(
early_stopping_params["monitor"], True, "validation_early_stopping")
return callbacks.EarlyStopping(**early_stopping_params)
def _create_train_early_stopping(
cfg_services: dict,
metrics_names: List[str]) -> callbacks.EarlyStopping:
"""Create an early stopping callback that monitors a training 'metric'.
Args:
cfg_services: dict, services subsection of config.
metrics_names: list[str], 'metrics' names.
Returns:
EarlyStopping, EarlyStopping callback that monitors a training 'metric'.
"""
early_stopping_params = cfg_services["train_early_stopping"]
early_stopping_params["monitor"] = _force_monitor_to_mode(
early_stopping_params["monitor"], metrics_names, False,
"train_early_stopping")
return callbacks.EarlyStopping(**early_stopping_params)
def get_callbacks(args):
"""Define callbacks for distributed training."""
callbacks = [
# This is necessary to ensure consistent initialization of all workers
hvd.callbacks.BroadcastGlobalVariablesCallback(0),
# Note: must be in the list before the ReduceLROnPlateau or other metrics-based callbacks.
hvd.callbacks.MetricAverageCallback(),
# Adjust Learning Rate
hvd.callbacks.LearningRateWarmupCallback(
warmup_epochs=args.warmup_epochs)
]
if args.train_only:
# Reduce learning rate on a schedule
onethirds_point = int(math.floor(args.epochs / 3))
twothirds_point = int(math.floor(args.epochs / 3 * 2))
callbacks.append(
hvd.callbacks.LearningRateScheduleCallback(
start_epoch=args.warmup_epochs,
end_epoch=onethirds_point,
multiplier=1.))
callbacks.append(
hvd.callbacks.LearningRateScheduleCallback(
start_epoch=onethirds_point,
end_epoch=twothirds_point,
multiplier=1e-1))
callbacks.append(
hvd.callbacks.LearningRateScheduleCallback(
start_epoch=twothirds_point,
end_epoch=args.epochs + 1,
multiplier=1e-2))
else:
# Reduce learning rate on validation loss plateau
callbacks.append(
cb.ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=5,
min_lr=0.001,
verbose=1 if hvd.rank() == 0 else 0))
if args.early_stopping:
callbacks.append(
cb.EarlyStopping(monitor='loss',
patience=7,
restore_best_weights=True))
print('Callbacks created on rank ' + str(hvd.rank()))
return callbacks
def callb(path_checkpoint):
callback_checkpoint = tf_cb.ModelCheckpoint(
filepath=path_checkpoint, monitor = 'loss', verbose=1,
save_weights_only=True, save_best_only=True)
callback_earlystopping = tf_cb.EarlyStopping(monitor='loss',
patience=20, verbose=1)
callback_reduce_lr = tf_cb.ReduceLROnPlateau(monitor='loss',
factor=0.98,
min_lr=0.3e-4,
patience=0,
verbose=1)
callBacks = [
callback_checkpoint,
callback_earlystopping,
callback_reduce_lr
]
return callBacks
def callableForTestEarlyStopping(model, test_obj, train_ds, num_epoch, steps,
strategy, saving_filepath, **kwargs):
class EpochCounterCallback(callbacks.Callback):
def on_epoch_begin(self, epoch, logs):
self.last_epoch = epoch
epoch_counter_cbk = EpochCounterCallback()
cbks = [
callbacks.EarlyStopping(
monitor='loss', min_delta=0.05, patience=1, verbose=1),
epoch_counter_cbk
]
# Empirically, it is expected that `model.fit()` would terminate around the
# 22th epoch. Asserting that it should have been stopped before the 50th
# epoch to avoid flakiness and be more predictable.
model.fit(x=train_ds, epochs=100, steps_per_epoch=steps, callbacks=cbks)
test_obj.assertLess(epoch_counter_cbk.last_epoch, 50)
def proc_early_stopping(test_obj):
class EpochCounterCallback(callbacks.Callback):
def on_epoch_begin(self, epoch, logs):
self.last_epoch = epoch
model, _, train_ds, steps = _model_setup(test_obj, file_format='')
epoch_counter_cbk = EpochCounterCallback()
cbks = [
callbacks.EarlyStopping(
monitor='loss', min_delta=0.05, patience=1, verbose=1),
epoch_counter_cbk
]
# Empirically, it is expected that `model.fit()` terminates around the
# 22th epoch. Asserting that it should have been stopped before the 50th
# epoch to avoid flakiness and be more predictable.
model.fit(x=train_ds, epochs=100, steps_per_epoch=steps, callbacks=cbks)
test_obj.assertLess(epoch_counter_cbk.last_epoch, 50)
def makeCb(self):
#images_validation, labels_validation = self.loadData(self.validation_dataset_filepath)
# Print the batch number at the beginning of every batch.
trainedbatch = []
batch_print_callback = callbacks.LambdaCallback(
on_batch_begin=lambda batch, logs: trainedbatch.append(batch))
# Stream the epoch loss to a file in JSON format. The file content
# is not well-formed JSON but rather has a JSON object per line.
json_log = open('loss_log.json', mode='wt', buffering=1)
json_logging_callback = callbacks.LambdaCallback(
on_epoch_end=lambda epoch, logs: json_log.write(
json.dumps({
'epoch': epoch,
'loss': logs['loss'],
'mae': logs['mean_absolute_error'],
'val_loss': logs['val_loss'],
'val_mae': logs['val_mean_absolute_error']
}) + '\n'),
on_train_end=lambda logs: json_log.close())
# Terminate some processes after having finished model training.
processes = []
cleanup_callback = callbacks.LambdaCallback(
on_train_end=lambda logs:
[p.terminate() for p in processes if p.is_alive()])
tensorboard = callbacks.TensorBoard(log_dir="logs/{}".format(time()))
callback = [
callbacks.EarlyStopping(monitor='val_loss',
patience=4,
mode='auto'), batch_print_callback,
json_logging_callback, cleanup_callback
]
return callback
def run_model(train_batches, validation_batches, num_classes):
feature_extractor = hub.KerasLayer(MODULE_HANDLE,
trainable=False,
input_shape=IMAGE_SIZE + (3, ),
output_shape=[FV_SIZE])
model = Sequential(
[feature_extractor,
Dense(num_classes, activation='softmax')])
optimizer = keras.optimizers.Adam(0.02)
loss = keras.losses.SparseCategoricalCrossentropy(from_logits=True)
model.compile(optimizer=optimizer, loss=loss, metrics=['accuracy'])
epochs = 50
callback = callbacks.EarlyStopping(monitor='val_loss',
patience=3,
restore_best_weights=True)
history = model.fit(train_batches,
epochs=epochs,
validation_data=validation_batches,
callbacks=callback,
verbose=True)
model.save('cat_vs_dog_model')
return model
def build_callbacks(self, conf, callbacks_list):
'''
The purpose of the method is to set up logging and history. It is based
on Keras Callbacks
https://github.com/fchollet/keras/blob/fbc9a18f0abc5784607cd4a2a3886558efa3f794/keras/callbacks.py
Currently used callbacks include: BaseLogger, CSVLogger, EarlyStopping.
Other possible callbacks to add in future: RemoteMonitor,
LearningRateScheduler
Argument list:
- conf: There is a "callbacks" section in conf.yaml file.
Relevant parameters are:
- list: Parameter specifying additional callbacks, read
in the driver script and passed as an argument of type list (see next
arg)
- metrics: List of quantities monitored during training and validation
- mode: one of {auto, min, max}. The decision to overwrite the current
save file is made based on either the maximization or the minimization
of the monitored quantity. For val_acc, this should be max, for
val_loss this should be min, etc. In auto mode, the direction is
automatically inferred from the name of the monitored quantity.
- monitor: Quantity used for early stopping, has to
be from the list of metrics
- patience: Number of epochs used to decide on whether to apply early
stopping or continue training
- callbacks_list: uses callbacks.list configuration parameter,
specifies the list of additional callbacks Returns: modified list of
callbacks
'''
mode = conf['callbacks']['mode']
monitor = conf['callbacks']['monitor']
patience = conf['callbacks']['patience']
csvlog_save_path = conf['paths']['csvlog_save_path']
# CSV callback is on by default
if not os.path.exists(csvlog_save_path):
os.makedirs(csvlog_save_path)
callbacks_list = conf['callbacks']['list']
callbacks = [cbks.BaseLogger()]
callbacks += [self.history]
callbacks += [
cbks.CSVLogger("{}callbacks-{}.log".format(
csvlog_save_path,
datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")))
]
if "earlystop" in callbacks_list:
callbacks += [
cbks.EarlyStopping(patience=patience,
monitor=monitor,
mode=mode)
]
if "lr_scheduler" in callbacks_list:
pass
return cbks.CallbackList(callbacks)
def rnn_train(space): #functional
''' train lightgbm booster based on training / validaton set -> give predictions of Y '''
params = space.copy()
lookback = 20 # lookback = 5Y * 4Q = 20Q
x_fields = 10 # lgbm top15 features -> 10 features in rnn
inputs_loss_weight = 0.1 # loss weights for individual outputs from each rnn model
dense_loss_weight = 2 # loss weights for final output
loss_weights = [inputs_loss_weight] * x_fields + [
dense_loss_weight
] # loss weights for training
loss = [args.objective] * (
x_fields + 1) # use MAE loss function for all inputs and final
metrics = [args.objective] * (x_fields + 1)
input_img = Input(shape=(lookback, x_fields))
outputs = []
states = []
for col in range(10): # build model for each feature
g_1 = K.expand_dims(
input_img[:, :, col], axis=2
) # add dimension to certain feature: shape = (samples, 20, 1)
for i in range(params['num_gru_layer']):
temp_nodes = int(
min(params['gru_nodes'] * (2**(params['gru_nodes_mult'] * i)),
8))
extra = dict(return_sequences=True)
if args.bi == False:
if i == params['num_gru_layer'] - 1:
extra = dict(return_sequences=False)
g_state = GRU(temp_nodes, **extra)(g_1) # forecast state
elif i == 0:
g_1 = GRU(temp_nodes, **extra)(g_1)
else:
g_1 = GRU(temp_nodes,
dropout=params['gru_dropout'],
**extra)(g_1)
else: # try bidirectional one
if i == params['num_gru_layer'] - 1:
extra = dict(return_sequences=False)
g_state = GRU(temp_nodes, **extra)(g_1) # forecast state
elif i == 0:
g_1 = Bidirectional(GRU(temp_nodes, **extra))(g_1)
else:
g_1 = Bidirectional(
GRU(temp_nodes, dropout=params['gru_dropout'],
**extra))(g_1)
g_output = Dense(1)(g_state)
states.append(g_state)
outputs.append(g_output)
f_x = Concatenate(axis=1)(states)
for i in range(
params['num_dense_layer']): # for second or third dense layers
f_x = Dense(10)(f_x)
f_x = Dense(1, name='final_dense')(f_x)
outputs.append(f_x)
model = Model(
inputs=input_img,
outputs=outputs) # outputs = 10 forecast states + final forecast
callbacks_list = [
callbacks.ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=10),
callbacks.EarlyStopping(monitor='val_loss', patience=10, mode='auto')
] # add callbacks
lr_val = 10**-int(params['learning_rate'])
adam = optimizers.Adam(lr=lr_val)
model.compile(adam, loss=loss, metrics=metrics, loss_weights=loss_weights)
model.summary()
history = model.fit(X_train, [Y_train] * (x_fields + 1),
epochs=50,
batch_size=params['batch_size'],
validation_data=(X_valid, [Y_valid] * (x_fields + 1)),
verbose=1,
callbacks=callbacks_list)
Y_test_pred = model.predict(X_test)[-1] # final dense predictions
Y_train_pred = model.predict(X_train)[-1]
Y_valid_pred = model.predict(X_valid)[-1]
return Y_test_pred, Y_train_pred, Y_valid_pred, history
def train(x_train, y_train, x_test, y_test, epochs):
# calculate classes
if np.unique(y_train).shape[0] == np.unique(y_test).shape[0]:
#
num_classes = np.unique(y_train).shape[0]
else:
print('Error in class data...')
return -2
# set validation data
'''val_size = int(0.1 * x_train.shape[0])
r = np.random.randint(0, x_train.shape[0], size=val_size)
x_val = x_train[r, :, :]
y_val = y_train[r]
x_train = np.delete(x_train, r, axis=0)
y_train = np.delete(y_train, r, axis=0)'''
step = int(x_train.shape[0] * 0.005)
length = int(x_train.shape[0] * 0.1 * 0.005)
r = []
for i in range(0, x_train.shape[0] - length, step):
r.extend(range(i, i + length))
x_val = x_train[r, :, :]
y_val = y_train[r]
x_train = np.delete(x_train, r, axis=0)
y_train = np.delete(y_train, r, axis=0)
print('\nInitializing CNN2D...')
print('\nclasses:', num_classes)
print('x train shape:',
x_train.shape), print('x val shape:',
x_val.shape), print('x test shape:',
x_test.shape)
print('y train shape:',
y_train.shape), print('y val shape:',
y_val.shape), print('y test shape:',
y_test.shape)
print("\nTrain split with mean|std {:.2f}|{:.2f}".format(
np.mean(x_train), np.std(x_train)))
print("Test split with mean|std {:.2f}|{:.2f}".format(
np.mean(x_test), np.std(x_test)))
# shape data
x_train = x_train.reshape(x_train.shape[0], x_train.shape[1],
x_train.shape[2], 1)
x_val = x_val.reshape(x_val.shape[0], x_val.shape[1], x_val.shape[2], 1)
x_test = x_test.reshape(x_test.shape[0], x_test.shape[1], x_test.shape[2],
1)
y_train = tf.keras.utils.to_categorical(y_train, num_classes)
y_val = tf.keras.utils.to_categorical(y_val, num_classes)
y_test = tf.keras.utils.to_categorical(y_test, num_classes)
# define the model
activation = 'elu'
regularizer = 0.0000
dropout = 0.25
# preprocessing
'''
offset = 1.0 * np.std(x_train)
dc0 = (x)
dc1 = GaussianNoise(offset*0.1)(x)
dc2 = GaussianDropout(dropout)(x)
dc3 = Lambda(lambda r: r + __import__('keras').backend.random_uniform((1,), -offset, offset))(x)
dc4 = Lambda(lambda r: r + __import__('keras').backend.random_uniform((1,), -offset, offset))(x)
m = Concatenate()([dc0, dc1, dc2, dc3, dc4])
m = Lambda(lambda r: r - __import__('keras').backend.mean(r))(x)
'''
# sequential
model = Sequential()
model.add(
Conv2D(16,
kernel_size=(3, 3),
strides=(2, 1),
activation='elu',
kernel_regularizer=regularizers.l2(regularizer),
input_shape=(x_train.shape[1], x_train.shape[2], 1)))
model.add(EntropyPooling2D(pool_size=(2, 2)))
model.add(Dropout(dropout))
model.add(
Conv2D(32,
kernel_size=(3, 3),
strides=(1, 1),
activation='elu',
kernel_regularizer=regularizers.l2(regularizer)))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Dropout(dropout))
model.add(
Conv2D(64,
kernel_size=(3, 3),
strides=(1, 1),
activation='elu',
kernel_regularizer=regularizers.l2(regularizer)))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Dropout(dropout))
# model.add(Conv2D(128, kernel_size=(3, 3), strides=(1, 1), activation='elu', kernel_regularizer=regularizers.l2(regularizer)))
# model.add(MaxPooling2D(pool_size=(1, 2)))
# model.add(Dropout(dropout))
model.add(Flatten())
model.add(
Dense(64,
activation='elu',
kernel_regularizer=regularizers.l2(regularizer)))
model.add(Dropout(dropout))
model.add(Dense(num_classes, activation='softmax'))
# functional
'''
x = Input((x_train.shape[1], x_train.shape[2], x_train.shape[3]))
m = Conv2D(16, 3, activation=activation , kernel_regularizer=regularizers.l2(regularizer))(x)
m = EntropyPooling2D((2, 2))(m)
m = Dropout(dropout)(m)
m = Conv2D(32, 3, activation=activation, kernel_regularizer=regularizers.l2(regularizer))(m)
m = EntropyPooling2D((2, 2))(m)
m = Dropout(dropout)(m)
m = Conv2D(64, 3, activation=activation, kernel_regularizer=regularizers.l2(regularizer))(m)
m = EntropyPooling2D((2, 2))(m)
m = Dropout(dropout)(m)
if x_train.shape[1] < 50:
#
m = Flatten()(m)
else:
m = Conv2D(128, 3, activation=activation, kernel_regularizer=regularizers.l2(regularizer))(m)
m = GlobalAveragePooling2D()(m)
m = Dropout(dropout)(m)
m = (Dense(64, activation=activation, kernel_regularizer=regularizers.l2(regularizer)))(m)
m = Dropout(dropout)(m)
y = Dense(num_classes, activation='softmax')(m)
model = Model(inputs=[x], outputs=[y])
'''
# summarize model
for i in range(0, len(model.layers)):
if i == 0:
plot_model(model, to_file='Models\\model_cnn2d.png')
# f = open('Models\\model_cnn2d.txt', 'w')
# print(' ')
# print('{}. Layer {} with input / output shapes: {} / {}'.format(i, model.layers[i].name, model.layers[i].input_shape, model.layers[i].output_shape))
# f.write('{}. Layer {} with input / output shapes: {} / {} \n'.format(i, model.layers[i].name, model.layers[i].input_shape, model.layers[i].output_shape))
if i == len(model.layers) - 1:
# f.close()
print(' ')
model.summary()
# compile, fit evaluate
callback = [
callbacks.EarlyStopping(monitor='val_acc',
min_delta=0.01,
patience=10,
restore_best_weights=True)
]
model.compile(loss=tf.keras.losses.categorical_crossentropy,
optimizer=tf.keras.optimizers.Adam(),
metrics=['accuracy'])
model.fit(x_train,
y_train,
batch_size=256,
epochs=epochs,
verbose=2,
validation_data=(x_val, y_val),
callbacks=callback)
score = model.evaluate(x_test, y_test, verbose=2)
# evaluate on larger frames
aggr_size = 5
for i in range(0, y_test.shape[0] - aggr_size, aggr_size):
if i == 0:
y_pred = model.predict(x_test)
y_pred = np.argmax(y_pred, axis=1)
y_test = np.argmax(y_test, axis=1)
y_aggr_test = []
y_aggr_pred = []
if np.unique(y_test[i:i + aggr_size]).shape[0] == 1:
y_aggr_test.append(stats.mode(y_test[i:i + aggr_size])[0][0])
y_aggr_pred.append(stats.mode(y_pred[i:i + aggr_size])[0][0])
# print(confusion_matrix(np.argmax(y_test, axis=1), np.argmax(y_pred, axis=1)))
scipy_score = classification_report(y_aggr_test,
y_aggr_pred,
output_dict=True)['accuracy']
print('short {:.2f} and aggr {:.2f}'.format(score[1], scipy_score))
# save model
open("Models\\model_cnn2d.json", "w").write(model.to_json())
pickle.dump(model.get_config(), open("Models\\model_cnn2d.pickle", "wb"))
model.save_weights("Models\\model_cnn2d.h5")
# results
return score[1]
def creat_net(train_generator, validation_generator, batch_size, image_lengh,
image_width):
base_model = applications.InceptionResNetV2(weights='imagenet',
include_top=False,
input_shape=(image_width,
image_lengh, 3))
for layer in base_model.layers:
layer.trainable = False
x = base_model.output
x = tf.keras.layers.Conv2D(128,
kernel_size=(3, 3),
strides=(1, 1),
activation='relu')(x)
x = tf.keras.layers.Dropout(0.2)(x)
x = tf.keras.layers.GlobalAveragePooling2D()(x)
x = tf.keras.layers.Dropout(0.2)(x)
x = tf.keras.layers.Dense(4, activation='softmax')(x)
model = Model(base_model.layers[0].input, x)
model.compile(optimizer='rmsprop',
loss='categorical_crossentropy',
metrics=['accuracy'])
#保存最优模型
filepath = './模型/InceptionResNetV2_weights-improvement-{epoch:02d}-{val_accuracy:.2f}.hdf5'
checkpoint = callbacks.ModelCheckpoint(filepath,
monitor='val_accuracy',
verbose=1,
save_best_only=True,
mode='max')
early = callbacks.EarlyStopping(monitor='val_loss',
min_delta=0,
patience=0,
verbose=0,
mode='auto',
baseline=None,
restore_best_weights=False)
model.fit_generator(train_generator,
epochs=30,
steps_per_epoch=1707 // batch_size,
validation_data=validation_generator,
validation_steps=264 // batch_size,
callbacks=[checkpoint, checkpoint]) #Reduce])
#绘制误差和准确率曲线
loss = model.history.history['loss']
val_loss = model.history.history['val_loss']
epoches = range(1, len(loss) + 1)
acc = model.history.history['accuracy']
val_acc = model.history.history['val_accuracy']
plt.subplot(121)
plt.plot(epoches, loss, 'bo', label='training_loss')
plt.plot(epoches, val_loss, 'r', label='validation_loss')
plt.xlabel('epoches')
plt.ylabel('loss')
plt.title('losses of train and val')
plt.legend()
plt.subplot(122)
plt.plot(epoches, acc, 'bo', label='training_acc')
plt.plot(epoches, val_acc, 'r', label='validation_acc')
plt.xlabel('epoches')
plt.ylabel('acc')
plt.title('accuracy of train and val')
plt.legend()
plt.show()
from GVHD_BAR.show_data import calc_results_and_plot
from GVHD_BAR.calculate_distances import calculate_distance
from GVHD_BAR.cluster_time_events import cluster_based_on_time
import os
SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
RECORD = True
PLOT = False
USE_SIMILARITY = False
USE_CLUSTER = False
USE_CLOSEST_NEIGHBOR = False
USE_CERTAINTY = False
PLOT_INPUT_TO_NN_STATS = False
callbacks_ = callbacks.EarlyStopping(monitor='my_mse_loss',
min_delta=0.5,
patience=10,
verbose=0, mode='auto')
# @autograph.convert()
def my_loss(y_true, y_pred):
mse_loss = my_mse_loss(y_true, y_pred)
time_sense_loss = y_true[:, 2] - y_pred[:, 1] # Max_delta - predicted_delta should be negative
tsls = time_sense_loss #tf.square(time_sense_loss)
return y_true[:, 4] * tsls + y_true[:, 3] * mse_loss
def my_mse_loss(y_true, y_pred):
mse_loss = tf.reduce_mean(tf.square(y_true[:, 1] - y_pred[:, 1]))
return mse_loss
# Build the model
model = inception_resnet_v2.build_inception_resnet_v2_notop(image_dimensions = (image_height, image_width, image_depth)
, pooling = None
, size_final_dense = 256
, num_classes = num_classes
, trainable = True
, weights = None
, final_regulariser = l1(0.01))
#model = multi_gpu_model(model, gpus=2)
print("MODEL BUILT")
# Now train it
opt_RMSprop = RMSprop(lr=0.0001)
model.compile(optimizer=opt_RMSprop,loss='categorical_crossentropy', metrics=['accuracy'])
callback_lr_plateau = callbacks.ReduceLROnPlateau(monitor='val_loss', factor=0.2, patience=5)
callback_earlystopping = callbacks.EarlyStopping(monitor='val_loss', patience=3)
print("MODEL COMPILED")
train_start = time.time()
os.makedirs(os.path.dirname(dir_tensorboard_logs), exist_ok=True) # Make tensorboard log directory
model.fit(dataset_train
, epochs=num_epochs
, steps_per_epoch=num_steps_per_epoch
, validation_data=dataset_valid
, validation_steps=num_steps_per_epoch_valid
, callbacks = [callback_tensorboard, callback_lr_plateau]
)
print("Training time: %s seconds" % (time.time() - train_start))
print(model.summary())
def train(self):
self.build_and_compile_model()
# Identify last version of trained model
files = get_checkpoint_file_list(self.config.checkpoint_dir,
self.config.model_name)
if not files:
model_number = self.config.model_name + "_0"
else:
# Resume training vs new training decision
if self.config.resume_train:
print("Resume training from previous checkpoint")
try:
self.recover_model_from_checkpoint()
model_number = self.model_version_number
except FileNotFoundError:
print("Model not found. Creating new model")
model_number = self.model_version_number
safe_mkdir_recursive(self.config.checkpoint_dir +
model_number)
else:
model_number = self.config.model_name + '_' + str(
int(files[-1].split('_')[-1]) + 1)
os.mkdir(self.config.checkpoint_dir + model_number)
self.trained_model_dir = self.config.checkpoint_dir + model_number + '/'
# Get training and validation datasets from saved files
dataset = self.get_dataset(train=True,
val_split=True,
random_split=False,
shuffle=True,
repeat_ds=True,
normalize=False)
train_ds, validation_ds, ds_lengths = dataset
train_steps_per_epoch = int(
math.ceil(ds_lengths[0] / self.config.batch_size))
val_steps_per_epoch = int(
math.ceil((ds_lengths[1] / self.config.batch_size)))
def lr_scheduler(epoch, lr):
decay_rate = 0.5
if epoch % self.config.lr_scheduler == 0 and epoch:
return lr * decay_rate
return lr
keras_callbacks = [
callbacks.EarlyStopping(patience=self.config.patience,
monitor='val_loss'),
callbacks.TensorBoard(write_images=True,
log_dir=self.config.checkpoint_dir +
model_number + "/keras",
histogram_freq=self.config.summary_freq),
callbacks.LearningRateScheduler(lr_scheduler, verbose=1),
CustomModelCheckpoint(filepath=os.path.join(
self.config.checkpoint_dir + model_number,
self.config.model_name + "_{epoch:02d}.h5"),
save_weights_only=True,
verbose=1,
period=self.config.save_freq,
extra_epoch_number=self.last_epoch_number +
1),
]
# Train!
self.trainable_model.fit(train_ds,
verbose=1,
epochs=self.config.max_epochs,
steps_per_epoch=train_steps_per_epoch,
validation_steps=val_steps_per_epoch,
validation_data=validation_ds,
callbacks=keras_callbacks)
activation=activation,
name=name))
model.add(layers.Dense(num_classes, activation='softmax'))
model.compile(
optimizer=optimizers.Adam(lr=learning_rate),
loss='categorical_crossentropy',
metrics=['accuracy'])
util.save_model_summary(model)
# Train
callbacks = [
callbacks.EarlyStopping(
monitor='val_acc',
patience=2),
callbacks.TensorBoard(
log_dir='logs',
histogram_freq=0,
batch_size=32,
write_graph=True,
write_grads=False,
write_images=False),
callbacks.ModelCheckpoint(
filepath='weights.{epoch:02d}-{val_loss:.2f}.hdf5'),
]
model.fit(
x=data.train.images,
y=data.train.labels,