def Cnn_test():
# initializing the network
network = Cnn(BATCH_SIZE)
network.getTheParas(MODEL_FILE)
# load the test data
_, _, test_imgs, _, _, test_label = util.load_data(MNIST_PATH, False)
log_string('------------start test-----------')
num_batch = test_imgs.shape[0] // BATCH_SIZE
start = 0
end = start + BATCH_SIZE
loss = 0.0
total_correct = 0.0
total_seen = 0
for n in range(num_batch):
log_string('testing {}/{}(batchs) completed!'.format(n + 1, num_batch))
current_img = test_imgs[start:end, ...]
current_label = test_label[start:end, ...]
start = end
end += BATCH_SIZE
predict_val, loss_val = network.forward(current_img, current_label)
correct = np.sum(predict_val == current_label)
total_correct += correct
loss += loss_val
total_seen += BATCH_SIZE
log_string('eval mean loss: {}'.format(loss / num_batch))
log_string('eval accuracy: {}'.format(total_correct / total_seen))
def __init__(self, model_name):
self.model_name = model_name
self.action_names = ['A', 'D', 'M', 'L', 'R']
self.num_actions = len(self.action_names)
self.memory = deque()
self.model = Cnn(self.model_name, self.memory)
self.target_model = Cnn(self.model_name, [], target=True)
# self.state = np.zeros([1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 1])
self.previous_states = np.zeros(
[1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 4])
self.previous_actions = np.zeros([4])
self.previous_actions.fill(2)
self.q_values = np.zeros(5)
self.action = 2
self.count_states = self.model.get_count_states()
self.delay_count = 0
self.epsilon_linear = LinearControlSignal(
start_value=EPSILON_GREEDY_START_PROB,
end_value=EPSILON_GREEDY_END_PROB,
repeat=False)
self.advantage = 0
self.value = 0
self.score = 0
def __init__(self,
learning=True,
epsilon=1,
alpha=0.1,
discount=1,
tolerance=0.01):
self.Q = dict()
self.Q1 = dict()
self.Q2 = dict()
self.s = states.States()
self.s.buildAllStates()
self.cnn = Cnn()
self.learning = learning
self.epsilon = epsilon
self.alpha = alpha
self.discount = discount
self.tolerance = tolerance
self.t = 2
self.convolutionLayersNumber = 0
self.poolingLayersNumber = 0
self.fullyConnectedLayersNumber = 0
self.convolutionLayersLimit = 3
self.poolingLayersLimit = 2
self.fullyConnectedLayersLimit = 2
self.actionsInitialState()
self.actionsConvolutionState()
self.actionsPoolingState()
self.actionsFullyConnectedState()
def test(metadata_file, dataset_dir, model_file):
generator = AudioGenerator(metadata_path=metadata_file,
dataset_path=dataset_dir,
batch_size=1)
vggvox_net = Cnn(model_file)
metrics = vggvox_net.evaluate_generator(
test_generator=generator.test(), test_steps=generator.get_test_steps())
print(
f"Loss {metrics[0]}, Top 1 Accuracy {metrics[1]}, Top 5 Accuracy {metrics[2]}"
)
def train(metadata_file, dataset_dir, checkpoint_file):
generator = AudioGenerator(metadata_path=metadata_file,
dataset_path=dataset_dir,
batch_size=20)
vggvox_net = Cnn()
vggvox_net.fit_generator(model_checkpoint_path=checkpoint_file,
train_generator=generator.train(),
train_steps=generator.get_training_steps(),
validation_generator=generator.validate(),
validation_steps=generator.get_validation_steps())
def reset(self, testing=False):
if testing == True:
self.epsilon = 0
self.alpha = 0
else:
self.convolutionLayersNumber = 0
self.poolingLayersNumber = 0
self.fullyConnectedLayersNumber = 0
self.epsilon = 0.9999 * self.t
del self.cnn
self.cnn = Cnn()
def test(self):
print('---------------Start Testing-----------')
convNet = ()
self.cnn = Cnn()
changeState = self.initial
convNet += (changeState, )
while changeState.name != states.TERMINATE:
changeState = self.getMaxQState(self.Q, changeState)
convNet += (changeState, )
print('TestingnConvnet', convNet)
score = self.cnn.buildModel(convNet)
print('TestScore', score)
def __init__(self):
conf_path_cnn = '/src/cnn/conf/cnn.yaml'
with open(conf_path_cnn, 'r') as fd:
self.conf = yaml.safe_load(fd)
self.batch_size = self.conf['testing']['batch_size']
self.checkpoint_path = self.conf['misc']['checkpoint_path']
self.logger = Logger
self.preProcessor = PreProcessor(Logger)
self.cnn = Cnn(Logger, conf_path_cnn, testing=True)
self.sess = tf.compat.v1.Session()
self.start()
def createBest(parameters):
allSeqInfo, allTurnCombs = parseData.getSeqInfo()
doneSeqs = []
testSeqs = []
nn_user = nnUser(parameters)
#Number of sequences with known structure and less than 3 alanines
validSet = helpers.validSet(allSeqInfo)
#Print to command line the current parameter information
helpers.printParamInfo(parameters, 0)
with tf.variable_scope("model0"):
model = Cnn(parameters)
#For each sequence, place it into the current batch. Then, when there are a
#"batch number" of sequences collected, train a convo network with them as
#the validation set. Then, measure the accuracy of the current network.
sess = tf.Session()
nn_user.genData([], "test")
times, costs, metTests, metTrains, metTestBest = \
nn_user.trainNet(sess,model,0,production=True,saveBest=True,outputCost=parameters.outputCost)
#Output the best metric average and corresponding hyperparameters to a file
#in the paramResults directory
helpers.writeParamInfo("model/", "testNum", parameters, metTestBest, 0)
sess.close()
def findWellStruct():
allSeqs = helpers.readAllSeqs()
shutil.rmtree("bestpredictions")
os.mkdir("bestpredictions")
names = os.listdir("model")
testname = ""
for name in names:
if name[0:4] == "test":
testname = name
best, parameters = hyperparams.getHyperParams("model/" + testname)
nn_user = nnUser(parameters)
tf.reset_default_graph()
with tf.variable_scope("model" + str(int(testname[7:10])), reuse=None):
model = Cnn(parameters)
saver = tf.train.Saver()
with tf.Session() as sess:
saver.restore(sess, "model/my_model_final.ckpt")
nn_user.predict(sess, model, allSeqs, "best")
def __init__(self, channels, classes, imagesize, **kwargs):
super(ModelCnn, self).__init__(channels, classes, imagesize, **kwargs)
self.layers = Cnn.get_layers(channels, classes, imagesize)
del self.conv
del self.resnet
del self.net
def __init__(self, num_sift_features, num_classes, sift):
super(Classifier, self).__init__()
# define the cnn model:
self.cnn = Cnn()
self.sift = sift
classifier_model = []
classifier_model += [nn.BatchNorm1d(num_features=192 * 5 * 5 + 1152)]
classifier_model += [nn.Linear(192 * 5 * 5 + 1152, 2976)]
classifier_model += [nn.Dropout(0.2)]
classifier_model += [nn.ReLU()]
classifier_model += [nn.Linear(2976, 1000)]
classifier_model += [nn.Dropout(0.2)]
classifier_model += [nn.ReLU()]
classifier_model += [nn.Linear(1000, 10)]
# classifier_model += [nn.Dropout(0.2)]
# classifier_model += [nn.ReLU()]
# classifier_model += [nn.Linear(864, 432)]
# classifier_model += [nn.Dropout(0.2)]
# classifier_model += [nn.ReLU()]
# classifier_model += [nn.Linear(432, 10)]
# classifier_model += [nn.Linear(192 * 6 * 6 + 1152, 192 * 6 * 6 + 1152)]
# classifier_model += [nn.ReLU()]
# classifier_model += [nn.Dropout(0.2)]
# classifier_model += [nn.Linear(192 * 6 * 6 + 1152, 1000)]
# classifier_model += [nn.ReLU()]
# classifier_model += [nn.Dropout(0.2)]
# classifier_model += [nn.Linear(1000, 10)]
#classifier_model += [nn.Softmax(dim=1)]
self.classifier = nn.Sequential(*classifier_model)
def main():
epochs = 100
#x, y = load_data(DATA_PATH, verbose=False, num_samples=5)
x = np.load('/global/scratch/alex_vlissidis/X.npz')['x']
y = np.load('/global/scratch/alex_vlissidis/y.npz')['y']
print("training data shapes:", x.shape, y.shape)
x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=0.2)
print("building model...")
print(x.shape)
print(y.shape[1])
model = Cnn(x.shape[1:], y.shape[1])
model.build()
history = model.train(x_train, y_train, epochs=epochs)
print("Saving model...")
model.model.save('models/model.h5')
print("Plotting...")
f, (ax1, ax2) = plt.subplots(2, 1)
ax1.plot(range(1, epochs + 1),
history.history['val_acc'],
'tab:blue',
label="validation accuracy")
ax1.plot(range(1, epochs + 1),
history.history['acc'],
'tab:red',
label="training accuracy")
ax2.plot(range(1, epochs + 1),
history.history['loss'],
'tab:orange',
label="loss")
ax2.plot(range(1, epochs + 1),
history.history['val_loss'],
'tab:green',
label="validation loss")
ax1.legend()
ax2.legend()
f.savefig('figures/training.png', dpi=300)
print("Done.")
def Cnn_train():
# initializing the network
network = Cnn(BATCH_SIZE)
# load the data
train_imgs, val_imgs, _, train_label, val_label, _ = util.load_data(MNIST_PATH)
for epoch in range(MAX_EPOCH):
# eval_one_epoch(network, val_imgs, val_label)
log_string('------------start train epoch {}/{}----------'.format(epoch, MAX_EPOCH))
train_one_epoch(network, train_imgs, train_label, epoch)
def findSingleSeq(testSeq):
names = os.listdir("model")
testname = ""
for name in names:
if name[0:4] == "test":
testname = name
best, parameters = hyperparams.getHyperParams("model/" + testname)
nn_user = nnUser(parameters)
tf.reset_default_graph()
with tf.variable_scope("model" + str(int(testname[7:10])), reuse=None):
model = Cnn(parameters)
saver = tf.train.Saver()
with tf.Session() as sess:
saver.restore(sess, "model/my_model_final.ckpt")
nn_user.predict(sess, model, [testSeq], "individ")
class Test:
def __init__(self):
conf_path_cnn = '/src/cnn/conf/cnn.yaml'
with open(conf_path_cnn, 'r') as fd:
self.conf = yaml.safe_load(fd)
self.batch_size = self.conf['testing']['batch_size']
self.checkpoint_path = self.conf['misc']['checkpoint_path']
self.logger = Logger
self.preProcessor = PreProcessor(Logger)
self.cnn = Cnn(Logger, conf_path_cnn, testing=True)
self.sess = tf.compat.v1.Session()
self.start()
def start(self):
test_x, test_y = self.preProcessor.get_data(testing=True)
self.logger.info('testing...')
# restore model
self.sess = tf.compat.v1.Session()
saver = tf.compat.v1.train.Saver()
model_path = self.conf['testing']['model']
saver.restore(self.sess, model_path)
self.logger.info('{0} restored'.format(model_path))
# test
self.sess.run(tf.compat.v1.local_variables_initializer())
pred_y, loss, acc = self.cnn.analyze_epoch(self.sess, test_x, test_y)
self.logger.info('test_loss: {0}, test_acc: {1}'.format(loss, acc))
self.sess.close()
return pred_y
class DeepTrafficAgent:
def __init__(self, model_name):
self.model_name = model_name
self.action_names = ['A', 'D', 'M', 'L', 'R']
self.num_actions = len(self.action_names)
self.memory = deque()
self.model = Cnn(self.model_name, self.memory)
self.target_model = Cnn(self.model_name, [], target=True)
# self.state = np.zeros([1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 1])
self.previous_states = np.zeros(
[1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 4])
self.previous_actions = np.zeros([4])
self.previous_actions.fill(2)
self.q_values = np.zeros(5)
self.action = 2
self.count_states = self.model.get_count_states()
self.delay_count = 0
self.epsilon_linear = LinearControlSignal(
start_value=EPSILON_GREEDY_START_PROB,
end_value=EPSILON_GREEDY_END_PROB,
repeat=False)
self.advantage = 0
self.value = 0
self.score = 0
def get_action_name(self, action):
return self.action_names[action]
def get_action_index(self, action):
return self.action_names.index(action)
def act(self, state, is_training=True):
state = state.reshape(VISION_F + VISION_B + 1,
VISION_W * 2 + 1).tolist()
previous_states = self.previous_states.tolist()
for n in range(len(previous_states)):
for y in range(len(previous_states[n])):
for x in range(len(previous_states[n][y])):
previous_states[n][y][x].pop(0)
previous_states[n][y][x].append(state[y][x])
self.previous_states = np.array(previous_states, dtype=int)
self.previous_states = self.previous_states.reshape(
1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 4)
self.previous_actions = np.roll(self.previous_actions, -1)
self.previous_actions[3] = self.action
self.q_values = self.model.get_q_values(self.previous_states,
self.previous_actions)
self.q_values = self.q_values[0][0]
if is_training and self.epsilon_linear.get_value(
iteration=self.model.get_count_states()) > uniform(0, 1):
# or (not is_training and EPSILON_GREEDY_TEST_PROB > uniform(0, 1)):
self.action = choice([0, 1, 2, 3, 4])
else:
self.action = np.argmax(self.q_values)
return self.q_values, self.get_action_name(self.action)
def remember(self,
reward,
next_state,
end_episode=False,
is_training=True):
next_state = next_state.reshape(VISION_F + VISION_B + 1,
VISION_W * 2 + 1).tolist()
previous_states = self.previous_states.tolist()
for n in range(len(previous_states)):
for y in range(len(previous_states[n])):
for x in range(len(previous_states[n][y])):
previous_states[n][y][x].pop(0)
previous_states[n][y][x].append(next_state[y][x])
next_state = np.array(previous_states).reshape(-1,
VISION_F + VISION_B + 1,
VISION_W * 2 + 1, 4)
next_actions = self.previous_actions.copy()
next_actions = np.roll(next_actions, -1)
next_actions[3] = self.action
self.count_states = self.model.get_count_states()
if is_training and self.model.get_count_states() > LEARN_START and len(
self.memory) > LEARN_START:
self.model.optimize(self.memory,
learning_rate=LEARNING_RATE,
batch_size=BATCH_SIZE,
target_network=self.target_model)
if self.model.get_count_states(
) % TARGET_NETWORK_UPDATE_FREQUENCY == 0:
self.model.save_checkpoint(self.model.get_count_states())
self.target_model.load_checkpoint()
self.model.log_target_network_update()
print("Target network updated")
elif self.model.get_count_states() % 1000 == 0:
self.model.save_checkpoint(self.model.get_count_states())
if len(self.memory) > MAX_MEM:
self.memory.popleft()
self.memory.append((self.previous_states, next_state, self.action,
reward - self.score, end_episode,
self.previous_actions, next_actions))
self.score = reward
if end_episode:
self.previous_states = np.zeros(
[1, VISION_F + VISION_B + 1, VISION_W * 2 + 1, 4])
self.previous_actions = np.zeros([4])
self.previous_actions.fill(2)
self.q_values = np.zeros(5)
self.action = 2
self.score = 0
self.count_states = self.model.increase_count_states()
def setUp(self) -> None:
self.subject = Cnn()
import signal
import matplotlib.pyplot as plt
import numpy as np
from keras.datasets import mnist
from cnn import Cnn
from plain.layers.flatten import Flatten
from plain.layers.maxPooling import MaxPooling
from plain.layers.softmax import Softmax
from vectorized.layers.conv2d import Conv2d
from vectorized.layers.fully_connected import FullyConnected
cnn = Cnn(300, 0.07)
def keyboard_interrupt_handler(signal, frame):
cnn.save()
exit(0)
def main():
plt.ion()
# cnn = Cnn.load("saved/cnn_12-28-2019_19-36")
(X_train, y_train), (X_test, y_test) = mnist.load_data()
labels = np.zeros((y_train.shape[0], 10, 1))
for index, x in enumerate(y_train):
labels[index, x] = [1]
images = X_train.reshape(
# %%
train_x = np.expand_dims(train_x, axis=1)
print(train_x[0])
plt.imshow(train_x[0][0])
per = np.random.permutation(train_x.shape[0]) # 打乱后的行号
rtrain_x = torch.from_numpy(train_x[per])
rtrain_y = torch.from_numpy(train_y[per]).squeeze()
print(per)
plt.figure()
plt.imshow(rtrain_x[0][0])
# %%
cnn = Cnn()
cnn.to(device)
print(cnn)
dummy_input = torch.randn(1, 1, 48, 48, device=device)
torch.onnx.export(cnn,
dummy_input,
"convnet.onnx",
verbose=True,
input_names=['input'],
output_names=['output'])
# %%
learn_rate = 3e-4
los = nn.CrossEntropyLoss()
loader = Loader(rtrain_x, 64, label=rtrain_y)
def train():
TIMESTAMP = "{0:%Y-%m-%d-%H-%M/}".format(datetime.now())
log.log_info('program start')
data, num_good, num_bad = util.load_train_data(num_data // 2)
log.log_debug('Data loading completed')
# resample
data, length = util.resample(data, 600)
data = util.reshape(data, length)
good_data_origin = data[:num_good, :]
bad_data_origin = data[num_good:, :]
# extract bad data for test and train
permutation = list(np.random.permutation(len(bad_data_origin)))
shuffled_bad_data = bad_data_origin[permutation, :]
test_bad_data = shuffled_bad_data[:int(num_bad * 0.3), :]
train_bad_data_origin = shuffled_bad_data[int(num_bad * 0.3):, :]
# extract corresponding good data for test and train
permutation = list(np.random.permutation(len(good_data_origin)))
shuffled_good_data = good_data_origin[permutation, :]
test_good_data = shuffled_good_data[:len(test_bad_data), :]
train_good_data = shuffled_good_data[len(test_bad_data):, :]
assert len(test_bad_data) == len(test_good_data)
# construct test data
test_y = np.array([1.] * len(test_good_data) + [0.] * len(test_bad_data), dtype=np.float).reshape(
(len(test_bad_data) + len(test_good_data), 1))
test_x = np.vstack((test_good_data, test_bad_data))
# expand the number of bad data for train
train_x = np.vstack((train_good_data, train_bad_data_origin))
train_y = np.array([1.] * len(train_good_data) + [0.] * len(train_bad_data_origin), dtype=np.float).reshape(
(len(train_bad_data_origin) + len(train_good_data), 1))
train_x, train_y, num_expand = util.expand(train_x, train_y)
# regularize
for i in range(len(train_x)):
train_x[i, :, 0] = util.regularize(train_x[i, :, 0])
train_x[i, :, 1] = util.regularize(train_x[i, :, 1])
train_x[i, :, 2] = util.regularize(train_x[i, :, 2])
for i in range(len(test_x)):
test_x[i, :, 0] = util.regularize(test_x[i, :, 0])
test_x[i, :, 1] = util.regularize(test_x[i, :, 1])
test_x[i, :, 2] = util.regularize(test_x[i, :, 2])
# random
train_x, train_y = util.shuffle_data(train_x, train_y)
log.log_debug('prepare completed')
log.log_info('convolution layers: ' + str(conv_layers))
log.log_info('filters: ' + str(filters))
log.log_info('full connected layers: ' + str(fc_layers))
log.log_info('learning rate: %f' % learning_rate)
log.log_info('keep prob: ' + str(keep_prob))
log.log_info('the number of expanding bad data: ' + str(num_expand))
log.log_info('mini batch size: ' + str(mini_batch_size))
if mini_batch_size != 0:
assert mini_batch_size <= len(train_x)
cnn = Cnn(conv_layers, fc_layers, filters, learning_rate)
(m, n_W0, n_C0) = train_x.shape
n_y = train_y.shape[1]
# construction calculation graph
cnn.initialize(n_W0, n_C0, n_y)
cost = cnn.cost()
optimizer = cnn.get_optimizer(cost)
predict, accuracy = cnn.predict()
init = tf.global_variables_initializer()
saver = tf.train.Saver()
with tf.Session() as sess:
# log for tensorboard
merged = tf.summary.merge_all()
train_writer = tf.summary.FileWriter("resource/tsb/train/" + TIMESTAMP, sess.graph)
test_writer = tf.summary.FileWriter("resource/tsb/test/" + TIMESTAMP)
if enable_debug:
sess = tf_debug.LocalCLIDebugWrapperSession(sess)
sess.run(init)
for i in range(1, num_epochs + 1):
if mini_batch_size != 0:
num_mini_batches = int(m / mini_batch_size)
mini_batches = util.random_mini_batches(train_x, train_y, mini_batch_size)
cost_value = 0
for mini_batch in mini_batches:
(mini_batch_x, mini_batch_y) = mini_batch
_, temp_cost = sess.run([optimizer, cost], feed_dict={cnn.x: mini_batch_x, cnn.y: mini_batch_y,
cnn.keep_prob: keep_prob})
cost_value += temp_cost
cost_value /= num_mini_batches
else:
_, cost_value = sess.run([optimizer, cost],
feed_dict={cnn.x: train_x, cnn.y: train_y, cnn.keep_prob: keep_prob})
# disable dropout
summary_train, train_accuracy = sess.run([merged, accuracy],
feed_dict={cnn.x: train_x, cnn.y: train_y,
cnn.keep_prob: 1})
summary_test, test_accuracy = sess.run([merged, accuracy],
feed_dict={cnn.x: test_x, cnn.y: test_y, cnn.keep_prob: 1})
train_writer.add_summary(summary_train, i - 1)
test_writer.add_summary(summary_test, i - 1)
if print_detail and (i % 10 == 0 or i == 1):
info = '\nIteration %d\n' % i + \
'Cost: %f\n' % cost_value + \
'Train accuracy: %f\n' % train_accuracy + \
'Test accuracy: %f' % test_accuracy
log.log_info(info)
# stop when test>0.95 and train>0.99
if test_accuracy >= 0.95 and train_accuracy >= 0.99:
info = '\nIteration %d\n' % i + \
'Cost: %f\n' % cost_value + \
'Train accuracy: %f\n' % train_accuracy + \
'Test accuracy: %f' % test_accuracy
log.log_info(info)
saver.save(sess, "resource/model/" + TIMESTAMP)
break
saver.save(sess, "resource/model/" + TIMESTAMP)
train_writer.close()
test_writer.close()
log.log_info('program end')
class Train:
def __init__(self):
conf_path_cnn = '/src/cnn/conf/cnn.yaml'
with open(conf_path_cnn, 'r') as fd:
self.conf = yaml.safe_load(fd)
# load configuration
self.num_epochs = self.conf['training']['epochs']
self.batch_size = self.conf['training']['batch_size']
self.checkpoint_path = self.conf['misc']['checkpoint_path']
self.logger = Logger
self.preProcessor = PreProcessor(Logger)
self.cnn = Cnn(Logger, conf_path_cnn)
self.sess = tf.compat.v1.Session()
self.start()
def start(self):
train_x, train_y, val_x, val_y = self.preProcessor.get_data()
self.sess.run(tf.compat.v1.global_variables_initializer())
self.sess.run(tf.compat.v1.local_variables_initializer())
saver = tf.compat.v1.train.Saver()
num_iterations = int(len(train_x) / self.batch_size)
self.logger.info('training...')
for epoch in range(self.num_epochs):
for iter_ in range(num_iterations):
batch_x = train_x[iter_ * self.batch_size:(iter_ + 1) *
self.batch_size, :]
batch_y = train_y[iter_ * self.batch_size:(iter_ + 1) *
self.batch_size, :]
self.sess.run(self.cnn.training,
feed_dict={
self.cnn.layer_input: batch_x,
self.cnn.ground_truth: batch_y
})
# train loss
_, loss_train, acc_train = self.cnn.analyze_epoch(
self.sess, train_x, train_y)
# val loss
_, loss_val, acc_val = self.cnn.analyze_epoch(
self.sess, val_x, val_y)
self.logger.info(
'epoch: {0}/{1}, loss_train: {2}, acc_train: {3}, loss_val: {4}, acc_val: {5}'
.format(epoch + 1, self.num_epochs, loss_train, acc_train,
loss_val, acc_val))
# save model
saved_path = saver.save(self.sess,
'{0}model.ckpt'.format(self.checkpoint_path))
self.logger.info('model saved in {0}'.format(saved_path))
self.sess.close()
def createTrainTestPred(parameters, testNum, save):
allSeqInfo, allTurnCombs = parseData.getSeqInfo()
doneSeqs = []
count = 0
testSeqs = []
nn_user = nnUser(parameters)
#Number of sequences with known structure and less than 3 alanines
numLessThree = len(helpers.validSet(allSeqInfo))
#Print to command line the current parameter information
helpers.printParamInfo(parameters, testNum)
with tf.variable_scope("model" + str(testNum)):
model = Cnn(parameters)
bestMetAvg = 0.0
batchNum = 0
#For each sequence, place it into the current batch. Then, when there are a
#"batch number" of sequences collected, train a convo network with them as
#the validation set. Then, measure the accuracy of the current network.
sess = tf.Session()
for seq in allSeqInfo:
if helpers.numAla(seq) < 3 and seq not in doneSeqs:
if parameters.verbose:
print seq
testSeqs.append(seq)
count += 1
doneSeqs.append(seq)
currSeq = seq
for i in range(5):
currSeq = currSeq[5] + currSeq[0:5]
doneSeqs.append(currSeq)
if count % parameters.batchSize == 0 or count == numLessThree:
batchNum += 1
nn_user.genData(testSeqs, "test")
times, costs, metTests, metTrains, metTestBest =\
nn_user.trainNet(sess,model,testNum,production=False,\
saveBest=save,outputCost=parameters.outputCost)
bestMetAvg += metTestBest * len(testSeqs) / len(
helpers.validSet(allSeqInfo))
if parameters.outputCost: #Output files of the training and testing accuracy
#over the training process
helpers.outputCostFile(times, costs, testNum, batchNum)
helpers.outputMetTest(times[0:len(metTests)], metTests,
parameters.metric, testNum, batchNum)
helpers.outputMetTrain(times[0:len(metTrains)], metTrains,
parameters.metric, testNum,
batchNum)
trainSeqs = helpers.createTrainSeqs(allSeqInfo, testSeqs)
nn_user.predict(sess, model, testSeqs, "test")
nn_user.predict(sess, model, trainSeqs, "train")
first = False
testSeqs = []
if not parameters.crossValid:
break
#Output the best metric average and corresponding hyperparameters to a file
#in the paramResults directory
helpers.writeParamInfo("paramResults/", "testNum", parameters, bestMetAvg,
testNum)
sess.close()
def train():
# initialize the number of epochs to train for, initia learning rate,
# and batch size
RANDOM_SEED = 12345
EPOCHS = 1000
INIT_LR = 1e-3
TRAINING_BATCH_SIZE = 32
IMAGE_SIZE = 64
NUM_CLASS = 2
MODEL_TYPE = "MobileNetV2"
TEST_SIZE = 0
# initialize the data and labels
print("[INFO] loading images...")
inputs = []
labels = []
# grab the image paths and randomly shuffle them
image_names = sorted(
os.listdir(os.path.join(base_path, 'Data', 'Training')))
image_paths = []
for image_name in image_names:
image_paths.append(
os.path.join(base_path, 'Data', 'Training', image_name))
random.shuffle(image_paths)
# loop over the input images
for image_path in image_paths:
# load the image, pre-process it, and store it in the data list
image = load_img(image_path, target_size=(IMAGE_SIZE, IMAGE_SIZE))
array_image = img_to_array(image)
inputs.append(array_image)
# extract the class label from the image path and update the
# labels list
image_name = image_path.split(os.path.sep)[-1]
type = image_name.split('_')[0]
if type == 'gato':
label = 1
elif type == 'nogato':
label = 0
labels.append(label)
# Convert labels to numpy
labels = np.array(labels)
# scale the raw pixel intensities to the range [0, 1]
inputs = np.array(inputs, dtype="float") / 255.0
"""ADD TEST"""
test_inputs = []
test_labels = []
# grab the image paths and randomly shuffle them
test_image_names = sorted(
os.listdir(os.path.join(base_path, 'Data', 'Validation')))
test_image_paths = []
for test_image_name in test_image_names:
test_image_paths.append(
os.path.join(base_path, 'Data', 'Validation', test_image_name))
random.shuffle(image_paths)
# loop over the input images
for test_image_path in test_image_paths:
if ".jpg" not in test_image_path:
continue
# load the image, pre-process it, and store it in the data list
image = load_img(test_image_path, target_size=(IMAGE_SIZE, IMAGE_SIZE))
array_image = img_to_array(image)
test_inputs.append(array_image)
# extract the class label from the image path and update the
# labels list
test_image_name = test_image_path.split(os.path.sep)[-1]
type = test_image_name.split('_')[0]
if type == 'gato':
label = 1
elif type == 'nogato':
label = 0
test_labels.append(label)
# Convert labels to numpy
test_labels = np.array(test_labels)
test_labels = to_categorical(test_labels, num_classes=NUM_CLASS)
# scale the raw pixel intensities to the range [0, 1]
test_inputs = np.array(test_inputs, dtype="float") / 255.0
"""END TEST"""
# partition the data into training and testing splits using 90% of
# the data for training and the remaining 10% for testing
(train_x, test_x, train_y,
test_y) = train_test_split(inputs,
labels,
test_size=TEST_SIZE,
random_state=RANDOM_SEED)
# convert the labels from integers to vectors
train_y = to_categorical(train_y, num_classes=NUM_CLASS)
test_y = to_categorical(test_y, num_classes=NUM_CLASS)
"""TEST"""
test_x = np.vstack((test_x, test_inputs))
test_y = np.vstack((test_y, test_labels))
"""END TEST"""
# # construct the image generator for data augmentation
data_gen_augmentation = ImageDataGenerator(horizontal_flip=True)
#data_gen_augmentation = ImageDataGenerator()
"""
Decomment to preview images augmented
data_gen_augmentation.fit(train_x)
# the .flow() command below generates batches of randomly transformed images
# and saves the results to the `preview/` directory
i = 0
for batch in data_gen_augmentation.flow(train_x, batch_size=1,
save_to_dir='preview', save_prefix='cat',
save_format='jpeg'):
i += 1
if i > 20:
break # otherwise the generator would loop indefinitely
return
"""
# initialize the model
print("[INFO] compiling model...")
# model = Cnn.build_transfer_learning(width=IMAGE_SIZE, height=IMAGE_SIZE, depth=3,
# classes=NUM_CLASS, type=MODEL_TYPE)
model = Cnn.build_custom(width=IMAGE_SIZE,
height=IMAGE_SIZE,
depth=3,
classes=NUM_CLASS)
plot_model(model, to_file='model_topology.png', show_shapes=True)
# optimizer = Adam(lr=INIT_LR, decay=INIT_LR / EPOCHS)
optimizer = Adam(lr=INIT_LR)
model.compile(loss="binary_crossentropy",
optimizer=optimizer,
metrics=["accuracy"])
# Callbacks
tensorboard = TensorBoard(log_dir='Graph',
histogram_freq=0,
write_graph=True,
write_images=True)
file_name = "epoch_{epoch:02d}_valLoss_{val_loss:.6f}.h5"
checkpoint = ModelCheckpoint(os.path.join("Models", "Training", file_name),
monitor='val_loss',
save_best_only=False)
callbacks = [checkpoint, tensorboard]
# train the network
print("[INFO] training network...")
steps_per_epoch = int(len(train_x) / TRAINING_BATCH_SIZE)
H = model.fit_generator(data_gen_augmentation.flow(
train_x, train_y, batch_size=TRAINING_BATCH_SIZE),
validation_data=(test_x, test_y),
steps_per_epoch=5,
epochs=EPOCHS,
verbose=1,
callbacks=callbacks)
# # save the model to disk
print("[INFO] serializing network...")
model.save('model.h5') # creates a HDFfile 'model.h5'
# Generate and save plots
save_loss_plot(H, 'plot_loss.png')
save_accuracy_plot(H, 'plot_accuracy.png')
class Agent(object):
def __init__(self,
learning=True,
epsilon=1,
alpha=0.1,
discount=1,
tolerance=0.01):
self.Q = dict()
self.Q1 = dict()
self.Q2 = dict()
self.s = states.States()
self.s.buildAllStates()
self.cnn = Cnn()
self.learning = learning
self.epsilon = epsilon
self.alpha = alpha
self.discount = discount
self.tolerance = tolerance
self.t = 2
self.convolutionLayersNumber = 0
self.poolingLayersNumber = 0
self.fullyConnectedLayersNumber = 0
self.convolutionLayersLimit = 3
self.poolingLayersLimit = 2
self.fullyConnectedLayersLimit = 2
self.actionsInitialState()
self.actionsConvolutionState()
self.actionsPoolingState()
self.actionsFullyConnectedState()
def reset(self, testing=False):
if testing == True:
self.epsilon = 0
self.alpha = 0
else:
self.convolutionLayersNumber = 0
self.poolingLayersNumber = 0
self.fullyConnectedLayersNumber = 0
self.epsilon = 0.9999 * self.t
del self.cnn
self.cnn = Cnn()
def actionsInitialState(self):
actions = dict()
self.initialActions = []
statesHere = self.s.conv + self.s.pool + self.s.fully + self.s.terminate
for eachState in statesHere:
self.initialActions.append(eachState)
actions[eachState] = 0.0
self.initial = state.InitialState()
self.Q[self.initial] = self.Q1[self.initial] = \
self.Q2[self.initial] = actions
def actionsConvolutionState(self):
actions = dict()
self.convolutionActions = []
statesHere = self.s.conv + self.s.pool + self.s.fully + self.s.terminate
for eachState in statesHere:
self.convolutionActions.append(eachState)
actions[eachState] = 0.0
statesHere = self.s.conv
for eachState in statesHere:
self.Q[eachState] = self.Q1[eachState] = \
self.Q2[eachState] = actions
def actionsPoolingState(self):
actions = dict()
self.poolingActions = []
statesHere = self.s.conv + self.s.fully + self.s.terminate
for eachState in statesHere:
self.poolingActions.append(eachState)
actions[eachState] = 0.0
statesHere = self.s.pool
for eachState in statesHere:
self.Q[eachState] = self.Q1[eachState] = \
self.Q2[eachState] = actions
def actionsFullyConnectedState(self):
actions = dict()
self.fullyConnectedActions = []
statesHere = self.s.fully + self.s.terminate
for eachState in statesHere:
self.fullyConnectedActions.append(eachState)
actions[eachState] = 0.0
statesHere = self.s.fully
for eachState in statesHere:
self.Q[eachState] = self.Q1[eachState] = \
self.Q2[eachState] = actions
def getMaxQValue(self, QTable, state):
#print('Debug::States for maxQ:',state)
if state.name == states.TERMINATE:
return 0.0
maxQ = max(QTable[state].items(), key=lambda x: x[1])[1]
return maxQ
def getMaxQState(self, QTable, state):
maxState = max(QTable[state].items(), key=lambda x: x[1])[0]
return maxState
def update_Q1_table(self, stateActionPair, reward):
#print('StateActionPair',stateActionPair)
#print('reward Here',reward)
for eachStateAction in stateActionPair:
print('Update for :', eachStateAction)
self.learn(eachStateAction[0], eachStateAction[1], reward)
def learn(self, state, action, reward):
print('State', state)
print('Action', action)
print('Q-value added', self.Q[state][action])
if self.learning and action.name != states.TERMINATE:
getMaxQValueOfNextState = self.getMaxQValue(self.Q,\
self.getMaxQState(self.Q,action))
#print('getMaxQValueOfNextState',getMaxQValueOfNextState)
#print('reward',reward)
self.Q[state][action] = ((1-self.alpha) * self.Q[state][action]) + \
(self.alpha*(reward +(self.discount * getMaxQValueOfNextState)))
else:
self.Q[state][action] = ((1 - self.alpha) * self.Q[state][action]) + \
(self.alpha * reward)
print('at learn', self.Q)
print('State', state)
print('Action', action)
print('Q-value added', self.Q[state][action])
print(
'====================================================================='
)
def chooseAction(self, actionItems, state):
if self.learning:
if self.epsilon > random.random():
action = random.choice(actionItems)
else:
action = max(self.Q[state].items(), key=lambda x: x[1])[0]
return action
def setInitialState(self, changeState):
if changeState.name == states.CONV:
self.convolutionLayersNumber += 1
elif changeState.name == states.POOL:
self.poolingLayersNumber += 1
elif changeState.name == states.FULLY:
self.fullyConnectedLayersNumber += 1
def update(self):
print('New Code')
while self.epsilon > self.tolerance:
#Begin trial
convNet = ()
stateAction = ()
changeState = self.initial
actionTaken = self.chooseAction(self.initialActions, changeState)
stateAction += ((changeState, actionTaken), )
changeState = actionTaken
convNet += (changeState, )
self.setInitialState(changeState)
#print('Initial Change state to be added', changeState)
while changeState.name != states.TERMINATE:
if changeState.name == states.CONV and \
self.convolutionLayersNumber<self.convolutionLayersLimit:
#print('states.CONV getting called')
actionTaken = self.chooseAction(self.convolutionActions,
changeState)
stateAction += ((changeState, actionTaken), )
changeState = actionTaken
self.convolutionLayersNumber += 1
elif changeState.name == states.POOL and \
self.poolingLayersNumber<self.poolingLayersLimit:
#print('states.POOL getting called')
actionTaken = self.chooseAction(self.poolingActions,
changeState)
stateAction += ((changeState, actionTaken), )
changeState = actionTaken
self.poolingLayersNumber += 1
elif changeState.name == states.FULLY and \
self.fullyConnectedLayersNumber<self.fullyConnectedLayersLimit:
#print('states.FULLY getting called')
actionTaken = self.chooseAction(self.fullyConnectedActions,
changeState)
stateAction += ((changeState, actionTaken), )
changeState = actionTaken
self.fullyConnectedLayersNumber += 1
print('FullyConnectedLayersNumber--->',
self.fullyConnectedLayersNumber)
else:
#print('Else getting called in agent')
actionTaken = self.s.terminate[0]
stateAction += ((changeState, actionTaken), )
changeState = actionTaken
print('Change state to be added', changeState)
convNet += (changeState, )
print('Convnet--->>>>', convNet)
score = self.cnn.buildModel(convNet)
print(score)
self.update_Q1_table(stateAction, score[1])
#print('Model Trained!!')
print('=======self.Q======', self.Q)
self.reset()
def test(self):
print('---------------Start Testing-----------')
convNet = ()
self.cnn = Cnn()
changeState = self.initial
convNet += (changeState, )
while changeState.name != states.TERMINATE:
changeState = self.getMaxQState(self.Q, changeState)
convNet += (changeState, )
print('TestingnConvnet', convNet)
score = self.cnn.buildModel(convNet)
print('TestScore', score)
def run(self, x, nbit, resolution, error):
nbits = str(nbit)
test_data = np.load("./data/" + nbits + "bit" + "/" + nbits + "bit" +
"_" + str(resolution) + "x" + str(resolution) +
"_test_images.npy")
train_data = np.load("./data/" + nbits + "bit" + "/" + nbits + "bit" +
"_" + str(resolution) + "x" + str(resolution) +
"_train_images.npy")
x = int(x)
if (error != 0):
test_data = np.array(
[self.pixel_bit_error(error, i, nbit) for i in test_data])
if (x == 1):
generations = input("enter the number of generations")
batchSize = input("enter the size of each batch")
generations = int(generations)
batchSize = int(batchSize)
Jesus = Cnn()
Jesus.run(train_data, test_data, resolution, error, generations,
batchSize)
if (x == 2):
if (error != 0):
train_data = np.array(
[self.pixel_bit_error(error, i, nbit) for i in train_data])
Jesus = Svm()
Jesus.run(train_data, test_data, resolution)
if (x == 3):
if (error != 0):
train_data = np.array(
[self.pixel_bit_error(error, i, nbit) for i in train_data])
k = input("k ?")
k = int(k)
Jesus = Knn(k)
Jesus.run(train_data, test_data, resolution)
if (x == 4):
Jesus = Caliente([], error)
batchSize = input("enter the size of each batch")
generations = input("enter the number of generations")
generations = int(generations)
batchSize = int(batchSize)
Jesus.run(train_data, test_data, resolution, generations,
batchSize)
def main(args):
batch_size = 128
ds_train, ds_test, info = load_data(batch_size)
image_shape = info.features["image"].shape
image_size = tf.reduce_prod(image_shape)
num_train_samples = info.splits["train"].num_examples
num_test_samples = info.splits["test"].num_examples
cnn = Cnn()
if "init_model" in args.cnn_mode:
cnn.create_model(batch_size=batch_size,
image_shape=image_shape,
feature_outputs=int(100))
if "train" in args.cnn_mode:
cnn.train(ds_train,
ds_test,
epochs=10,
steps_per_epoch=int(num_train_samples / batch_size))
if "save" in args.cnn_mode:
cnn.save()
if "load" in args.cnn_mode:
cnn.load_combined_model()
if "test" in args.cnn_mode:
cnn.test(ds_test)
gp = DeepKernelGP(ds_train,
num_train_samples,
image_size,
10,
cnn.feature_extractor,
num_inducing_points=100)
if "train" in args.gp_mode:
gp.train(10000)
if "test" in args.gp_mode:
gp.test(ds_test, image_size, batch_size, num_test_samples)
import numpy as np
from tqdm import tqdm
from cnn import Cnn
from config import Config
from hyperparameters import Hyperparameters
import matplotlib.pyplot as plt
if __name__ == "__main__":
cfg = Config()
data = np.load(cfg.trainingDataName, allow_pickle=True)
metaData = np.load(cfg.trainingMetadataName, allow_pickle=True)
numSubjects = len(metaData[0])
print("Dataset Loaded")
hyp = Hyperparameters()
cnn = Cnn(cfg, hyp, numSubjects)
print("CNN Generated")
images = ((torch.from_numpy(np.stack(data[:, 0]))).view(
-1, cfg.imagChannels, cfg.res[0], cfg.res[1]))
oneHotVecs = torch.Tensor(list(data[:, 1]))
print("Images Converted to Tensors")
trainSize = int((1 - cfg.testPercent) * len(data))
testSize = len(data) - trainSize
trainImgs = images[:trainSize]
trainOneHotVecs = oneHotVecs[:trainSize]
testImgs = images[trainSize:]
testOneHotVecs = oneHotVecs[trainSize:]
import tensorflow as tf
from cnn import Cnn
import config
import util
x_train_orig, y_train_orig, x_test_orig, y_test_orig, classes = util.load_data_set(
)
x_train = util.pre_treat(x_train_orig)
x_test = util.pre_treat(x_test_orig)
y_train = util.pre_treat(y_train_orig, is_x=False, class_num=len(classes))
y_test = util.pre_treat(y_test_orig, is_x=False, class_num=len(classes))
cnn = Cnn(config.conv_layers, config.fc_layers, config.filters,
config.learning_rate, config.beta1, config.beta2)
(m, n_H0, n_W0, n_C0) = x_train.shape
n_y = y_train.shape[1]
# construction calculation graph
cnn.initialize(n_H0, n_W0, n_C0, n_y)
cnn.forward()
cost = cnn.cost()
optimizer = cnn.get_optimizer(cost)
predict, accuracy = cnn.predict()
init = tf.global_variables_initializer()
with tf.Session() as sess:
sess.run(init)
for i in range(1, config.num_epochs + 1):
def __init__(self):
# Keep a reference to the "close" line in the data[0] dataseries
self.dataclose = self.datas[0].close
self.dataopen = self.datas[0].open
self.datahigh = self.datas[0].high
self.datalow = self.datas[0].low
self.datavolume = self.datas[0].volume
#initialize cnns
self.cnns = []
for i in range(1):
filename = '/home/gene/git/autoTrading/backtrader/model/' + self.getdatanames(
)[0] + str(i) + '.h5'
self.cnns.append(Cnn(filename))
# Add a MovingAverageSimple indicator
self.rsi60 = bt.indicators.RSI_Safe(self.datas[0], period=100)
self.history = []
self.holding_days = []
self.indicator_count = 15
self.indicators = []
for i in range(self.indicator_count):
self.indicators.append([])
for i in range(6, 21):
j = 0
self.indicators[j].append(
bt.indicators.RSI_Safe(self.datas[0], period=i)) # momentum
j += 1
self.indicators[j].append(
bt.indicators.WilliamsR(self.datas[0], period=i)) # momentum
j += 1
self.indicators[j].append(
bt.talib.MFI(self.datahigh,
self.datalow,
self.dataclose,
self.datavolume,
period=i)) # momentum
j += 1
self.indicators[j].append(
bt.indicators.RateOfChange(self.datas[0],
period=i)) # momentum
j += 1
self.indicators[j].append(bt.talib.CMO(self.dataclose,
period=i)) # momentum
j += 1
self.indicators[j].append(bt.talib.SMA(self.dataclose, period=i))
j += 1
self.indicators[j].append(bt.talib.SMA(self.dataopen, period=i))
j += 1
self.indicators[j].append(
bt.indicators.ExponentialMovingAverage(self.datas[0],
period=i))
j += 1
self.indicators[j].append(
bt.indicators.WeightedMovingAverage(self.datas[0], period=i))
j += 1
self.indicators[j].append(
bt.indicators.HullMovingAverage(self.datas[0], period=i))
j += 1
self.indicators[j].append(
bt.indicators.Trix(self.datas[0], period=i)) # trend
j += 1
self.indicators[j].append(
bt.indicators.CommodityChannelIndex(self.datas[0],
period=i)) # trend
j += 1
self.indicators[j].append(
bt.indicators.DetrendedPriceOscillator(self.datas[0],
period=i)) # trend
j += 1
self.indicators[j].append(
bt.indicators.DirectionalMovementIndex(self.datas[0],
period=i)) # trend
j += 1
self.indicators[j].append(
bt.indicators.BollingerBands(self.datas[0],
period=i)) # volatility
j += 1