def gen_iterators(self):
(X_train, y_train, test) = self.load_data()
train = ArrayIterator(X_train, y_train, nclass=1000, lshape=(3, 224, 224))
test = ArrayIterator(X_train, y_train, nclass=1000, lshape=(3, 224, 224))
self._data_dict = {'train': train,
'valid': test}
return self._data_dict
def gen_iterators(self):
if self.filepath is None:
self.load_data()
data = pad_data(self.filepath,
vocab_size=self.vocab_size,
sentence_length=self.sentence_length)
(X_train, y_train), (X_test, y_test), nclass = data
self._data_dict = {'nclass': nclass}
self._data_dict['train'] = ArrayIterator(X_train, y_train, nclass=2)
self._data_dict['test'] = ArrayIterator(X_test, y_test, nclass=2)
return self._data_dict
def gen_iterators(self):
train = ArrayIterator(self.train_x,
self.train_y,
lshape=self.shape,
make_onehot=False,
name='train')
valid = ArrayIterator(self.valid_x,
self.valid_y,
lshape=self.shape,
make_onehot=False,
name='valid')
self._data_dict = {'train': train, 'valid': valid}
return self._data_dict
def gen_iterators(self):
(X_train, y_train), (X_test, y_test), nclass = self.load_data()
train = ArrayIterator(X_train,
y_train,
nclass=nclass,
lshape=(1, 28, 28),
name='train')
val = ArrayIterator(X_test,
y_test,
nclass=nclass,
lshape=(1, 28, 28),
name='valid')
self._data_dict = {'train': train, 'valid': val}
return self._data_dict
def gen_iterators(self):
datasets = self.load_data()
(X_train, y_train), (X_test, y_test), nclass = datasets
if self.pad_classes:
nclass = 16
train = ArrayIterator(X_train,
y_train,
nclass=nclass,
lshape=(3, 32, 32),
name='train')
test = ArrayIterator(X_test,
y_test,
nclass=nclass,
lshape=(3, 32, 32),
name='valid')
self._data_dict = {'train': train, 'valid': test}
return self._data_dict
def run(self):
global camera, autonomous_override
open_camera()
while True:
if not autonomous:
debug_print("Exiting autonomous thread")
close_camera()
turn_off_motors()
break
if autonomous_override:
time.sleep(0)
continue
# Grab a still frame
stream = picamera.array.PiRGBArray(camera)
camera.capture(stream, 'rgb', use_video_port=False)
debug_print("Grabbed a still frame")
debug_start_timing()
image = Image.fromarray(stream.array)
image = image.resize(size, Image.ANTIALIAS)
if (debug):
image.save(my_dir + "train/debug/capture" + str(self.cnt) + ".png", "PNG")
self.cnt = self.cnt + 1
r, g, b = image.split()
image = Image.merge("RGB", (b, g, r))
image = np.asarray(image, dtype=np.float32)
image = np.transpose(image, (2, 0, 1))
x_new = image.reshape(1, 3*W*H) - 127
if autonomous_override:
time.sleep(0)
continue
# Run neural network
inference_set = ArrayIterator(x_new, None, nclass=nclasses, lshape=(3, H, W))
out = model.get_outputs(inference_set)
debug_stop_timing()
decision = out.argmax()
debug_print(class_names[decision])
if not autonomous_override:
drive(decision)
def test_recognition(test_file_name):
# Load image
image = Image.open(test_file_name)
image.show()
print("Loaded " + test_file_name)
# Convert image to sample
image = image.resize(size, Image.ANTIALIAS)
r, g, b = image.split()
image = Image.merge("RGB", (b, g, r))
image = np.asarray(image, dtype=np.float32)
image = np.transpose(image, (2, 0, 1))
x_new = image.reshape(1, L) - 127
# Run neural network
inference_set = ArrayIterator(x_new,
None,
nclass=nclasses,
lshape=(3, H, W))
out = model.get_outputs(inference_set)
print "Recognized as " + class_names[out.argmax()]
def run(self):
while True:
if not autonomous:
debug_print("Exiting autonomous thread")
break
# Grab a still frame
stream = picamera.array.PiRGBArray(camera)
camera.capture(stream, 'rgb', use_video_port=True)
start_time = time.time()
debug_print("Grabbed a still frame")
image = Image.fromarray(stream.array)
image = image.resize(size, Image.ANTIALIAS)
if (debug):
image.save(
my_dir + "train/debug/capture" + str(self.cnt) + ".png",
"PNG")
self.cnt = self.cnt + 1
r, g, b = image.split()
image = Image.merge("RGB", (b, g, r))
image = np.asarray(image, dtype=np.float32)
image = np.transpose(image, (2, 0, 1))
x_new = image.reshape(1, 3 * W * H) - 127
# Run neural network
inference_set = ArrayIterator(x_new,
None,
nclass=nclasses,
lshape=(3, H, W))
out = model.get_outputs(inference_set)
debug_print("--- %s seconds per decision --- " %
(time.time() - start_time))
decision = out.argmax()
debug_print(class_names[decision])
send_cmd(decision)
# setup backend
be = gen_backend(**extract_valid_args(args, gen_backend))
# make dataset
path = load_imdb(path=args.data_dir)
(X_train,
y_train), (X_test, y_test), nclass = pad_data(path,
vocab_size=vocab_size,
sentence_length=sentence_length)
print "Vocab size - ", vocab_size
print "Sentence Length - ", sentence_length
print "# of train sentences", X_train.shape[0]
print "# of test sentence", X_test.shape[0]
train_set = ArrayIterator(X_train, y_train, nclass=2)
valid_set = ArrayIterator(X_test, y_test, nclass=2)
# weight initialization
uni = Uniform(low=-0.1 / embedding_dim, high=0.1 / embedding_dim)
g_uni = GlorotUniform()
if args.rlayer_type == 'lstm':
rlayer = LSTM(hidden_size,
g_uni,
activation=Tanh(),
gate_activation=Logistic(),
reset_cells=True)
elif args.rlayer_type == 'bilstm':
rlayer = DeepBiLSTM(hidden_size,
g_uni,
def __init__(self,
X_dict,
time_steps,
forward=1,
return_sequences=True,
randomize=False):
"""
Implements loading of given data into backend tensor objects. If the backend is specific
to an accelerator device, the data is copied over to that device.
Args:
X (ndarray): Input sequence with feature size within the dataset.
Shape should be specified as (num examples, feature size]
time_steps (int): The number of examples to be put into one sequence.
forward (int, optional): how many forward steps the sequence should predict. default
is 1, which is the next example
return_sequences (boolean, optional): whether the target is a sequence or single step.
Also determines whether data will be formatted
as strides or rolling windows.
If true, target value be a sequence, input data
will be reshaped as strides. If false, target
value will be a single step, input data will be
a rolling_window
"""
def rolling_window(spikes, stim, lag):
"""
Convert a into time-lagged vectors
a : (n, p)
lag : time steps used for prediction
returns (n-lag+1, lag, p) array
(Building time-lagged vectors is not necessary for neon.)
"""
assert spikes.shape[0] > lag
assert stim.shape[0] > lag
spikes_shape = [spikes.shape[0] - lag + 1, lag, spikes.shape[-1]]
stim_shape = [stim.shape[0] - lag + 1, lag, stim.shape[-1]]
spikes_strides = [
spikes.strides[0], spikes.strides[0], spikes.strides[-1]
]
stim_strides = [stim.strides[0], stim.strides[0], stim.strides[-1]]
spikes_out = np.lib.stride_tricks.as_strided(
spikes, shape=spikes_shape, strides=spikes_strides)
stim_out = np.lib.stride_tricks.as_strided(stim,
shape=stim_shape,
strides=stim_strides)
return {'spikes': spikes_out, 'stim': stim_out}
self.seq_length = time_steps
self.forward = forward
self.batch_index = 0
self.nfeatures = self.nclass = X_dict['spikes'].shape[1]
self.nsamples = X_dict['spikes'].shape[0]
self.shape = (self.nfeatures, time_steps)
self.return_sequences = return_sequences
self.mean = X_dict['spikes'].mean(axis=0)
target_steps = time_steps if return_sequences else 1
# pre-allocate the device buffer to provide data for each minibatch
# buffer size is nfeatures x (times * batch_size), which is handled by
# backend.iobuf()
self.X_dev = self.be.iobuf((self.nfeatures, time_steps))
self.y_dev = self.be.iobuf((self.nfeatures, target_steps))
if return_sequences is True:
# truncate to make the data fit into multiples of batches
extra_examples = self.nsamples % (self.be.bsz * time_steps)
if extra_examples:
X_dict['spikes'] = X_dict['spikes'][:-extra_examples]
X_dict['stim'] = X_dict['stim'][:-extra_examples]
# calculate how many batches
self.nsamples -= extra_examples
self.nbatches = self.nsamples // (self.be.bsz * time_steps)
self.ndata = self.nbatches * self.be.bsz * time_steps # no leftovers
# y is the lagged version of X
y = np.concatenate((X[forward:], X[:forward]))
self.y_series = y
# reshape this way so sequence is continuous along the batches
self.X = X.reshape(self.be.bsz, self.nbatches, time_steps,
self.nfeatures)
self.y = y.reshape(self.be.bsz, self.nbatches, time_steps,
self.nfeatures)
else:
X_dict['lag'] = time_steps
self.X = rolling_window(**X_dict)
self.X['spikes'] = self.X['spikes'][:-1]
self.X['stim'] = self.X['stim'][:-1]
self.y = X_dict['spikes'][time_steps:]
self.nsamples = self.X['spikes'].shape[0]
extra_examples = self.nsamples % (self.be.bsz)
if extra_examples:
self.X['spikes'] = self.X['spikes'][:-extra_examples]
self.X['stim'] = self.X['stim'][:-extra_examples]
self.y = self.y[:-extra_examples]
# calculate how many batches
self.nsamples -= extra_examples
self.nbatches = self.nsamples // self.be.bsz
self.ndata = self.nbatches * self.be.bsz
self.y_series = self.y
self.spike_series = self.X['spikes']
self.stim_series = self.X['stim']
Xshape = (self.nbatches, self.be.bsz, time_steps, self.nfeatures)
Yshape = (self.nbatches, self.be.bsz, 1, self.nfeatures)
#self.X = self.X.reshape(Xshape).transpose(1, 0, 2, 3)
#self.y = self.y.reshape(Yshape).transpose(1, 0, 2, 3)
return ArrayIterator(X=[self.spike_series, self.stim_series],
y=self.y_series,
make_onehot=False)
print("Loaded " + test_file_name)
image.show()
image = image.resize(size, Image.ANTIALIAS)
r, g, b = image.split()
image = Image.merge("RGB", (b, g, r))
image = np.asarray(image, dtype=np.float32)
image = np.transpose(image, (2, 0, 1))
return image.reshape(1, L) - 127
x_new[0] = load_sample(iamge_dir + "forward.jpg")
x_new[1] = load_sample(image_dir + "right.jpg")
x_new[2] = load_sample(image_dir + "left.jpg")
x_new[3] = load_sample(image_dir + "backward.jpg")
# Run neural network
inference_set = ArrayIterator(x_new, None, nclass=nclasses, lshape=(3, H, W))
out = mlp.get_outputs(inference_set)
# print out
print(class_names[out[0].argmax()])
print(class_names[out[1].argmax()])
print(class_names[out[2].argmax()])
print(class_names[out[3].argmax()])
# Sanity check 2
out = mlp.get_outputs(test)
print "Validation set result:"
print(out.argmax(1))
print "Compare the above to ground truth in dora/train/neon/val_file.csv.gz"
def benchmark(self):
for d in self.devices:
b = d if (self.backends is None) or (
"mkl" not in self.backends) else "mkl"
print("Use {} as backend.".format(b))
# Common suffix
suffix = "neon_{}_{}_{}by{}_{}".format(b, self.dataset,
self.resize_size[0],
self.resize_size[1],
self.preprocessing)
# Set up backend
# backend: 'cpu' for single cpu, 'mkl' for cpu using mkl library, and 'gpu' for gpu
be = gen_backend(backend=b,
batch_size=self.batch_size,
rng_seed=542,
datatype=np.float32)
# Prepare training/validation/testing sets
neon_train_set = ArrayIterator(X=np.asarray(
[t.flatten().astype('float32') / 255 for t in self.x_train]),
y=np.asarray(self.y_train),
make_onehot=True,
nclass=self.class_num,
lshape=(3, self.resize_size[0],
self.resize_size[1]))
neon_valid_set = ArrayIterator(X=np.asarray(
[t.flatten().astype('float32') / 255 for t in self.x_valid]),
y=np.asarray(self.y_valid),
make_onehot=True,
nclass=self.class_num,
lshape=(3, self.resize_size[0],
self.resize_size[1]))
neon_test_set = ArrayIterator(X=np.asarray([
t.flatten().astype('float32') / 255 for t in self.testImages
]),
y=np.asarray(self.testLabels),
make_onehot=True,
nclass=self.class_num,
lshape=(3, self.resize_size[0],
self.resize_size[1]))
# Initialize model object
self.neon_model = SelfModel(layers=self.constructCNN())
# Costs
neon_cost = GeneralizedCost(costfunc=CrossEntropyMulti())
# Model summary
self.neon_model.initialize(neon_train_set, neon_cost)
print(self.neon_model)
# Learning rules
neon_optimizer = SGD(0.01,
momentum_coef=0.9,
schedule=ExpSchedule(0.2))
# neon_optimizer = RMSProp(learning_rate=0.0001, decay_rate=0.95)
# # Benchmark for 20 minibatches
# d[b] = self.neon_model.benchmark(neon_train_set, cost=neon_cost, optimizer=neon_optimizer)
# Reset model
# self.neon_model = None
# self.neon_model = Model(layers=layers)
# self.neon_model.initialize(neon_train_set, neon_cost)
# Callbacks: validate on validation set
callbacks = Callbacks(
self.neon_model,
eval_set=neon_valid_set,
metric=Misclassification(3),
output_file="./saved_data/{}/{}/callback_data_{}.h5".format(
self.network_type, d, suffix))
callbacks.add_callback(
SelfCallback(eval_set=neon_valid_set,
test_set=neon_test_set,
epoch_freq=1))
# Fit
start = time.time()
self.neon_model.fit(neon_train_set,
optimizer=neon_optimizer,
num_epochs=self.epoch_num,
cost=neon_cost,
callbacks=callbacks)
print("Neon training finishes in {:.2f} seconds.".format(
time.time() - start))
# Result
# results = self.neon_model.get_outputs(neon_valid_set)
# Print error on validation set
start = time.time()
neon_error_mis = self.neon_model.eval(
neon_valid_set, metric=Misclassification()) * 100
print(
'Misclassification error = {:.1f}%. Finished in {:.2f} seconds.'
.format(neon_error_mis[0],
time.time() - start))
# start = time.time()
# neon_error_top3 = self.neon_model.eval(neon_valid_set, metric=TopKMisclassification(3))*100
# print('Top 3 Misclassification error = {:.1f}%. Finished in {:.2f} seconds.'.format(neon_error_top3[2], time.time() - start))
# start = time.time()
# neon_error_top5 = self.neon_model.eval(neon_valid_set, metric=TopKMisclassification(5))*100
# print('Top 5 Misclassification error = {:.1f}%. Finished in {:.2f} seconds.'.format(neon_error_top5[2], time.time() - start))
self.neon_model.save_params("./saved_models/{}/{}/{}.prm".format(
self.network_type, d, suffix))
# Print error on test set
start = time.time()
neon_error_mis_t = self.neon_model.eval(
neon_test_set, metric=Misclassification()) * 100
print(
'Misclassification error = {:.1f}% on test set. Finished in {:.2f} seconds.'
.format(neon_error_mis_t[0],
time.time() - start))
# start = time.time()
# neon_error_top3_t = self.neon_model.eval(neon_test_set, metric=TopKMisclassification(3))*100
# print('Top 3 Misclassification error = {:.1f}% on test set. Finished in {:.2f} seconds.'.format(neon_error_top3_t[2], time.time() - start))
# start = time.time()
# neon_error_top5_t = self.neon_model.eval(neon_test_set, metric=TopKMisclassification(5))*100
# print('Top 5 Misclassification error = {:.1f}% on test set. Finished in {:.2f} seconds.'.format(neon_error_top5_t[2], time.time() - start))
cleanup_backend()
self.neon_model = None
y,
train_size=0.9,
random_state=42)
print(X_train.shape, 'X train shape')
print(y_train.shape, 'y train shape')
parser = NeonArgparser(__doc__)
parser.add_argument('--kbatch',
type=int,
default=1,
help='number of data batches per noise batch in training')
args = parser.parse_args()
gen_backend(backend='cpu', batch_size=10)
train_set = ArrayIterator(X=X_train,
y=y_train,
nclass=2,
lshape=(1, 25, 25, 25))
valid_set = ArrayIterator(X=X_test, y=y_test, nclass=2)
gen_backend(backend='cpu', batch_size=10)
train_set = ArrayIterator(X=X_train,
y=y_train,
nclass=2,
lshape=(1, 25, 25, 25))
valid_set = ArrayIterator(X=X_test, y=y_test, nclass=2)
init = Gaussian(scale=0.01)
# discriminiator using convolution layers
lrelu = Rectlin(slope=0.1) # leaky relu for discriminator
# sigmoid = Logistic() # sigmoid activation function
print(np.max(X), 'max element')
print(np.min(X), 'min element')
# X -= mean
print(X.shape, 'X shape')
#print(np.max(X),'max element')
#print(np.min(X),'min element')
X_train, X_test, y_train, y_test = train_test_split(X,
y,
train_size=0.9,
random_state=42)
print(X_train.shape, 'X train shape')
print(y_train.shape, 'y train shape')
gen_backend(backend='gpu', batch_size=100)
train_set = ArrayIterator(X=X_train,
y=y_train,
nclass=2,
lshape=(1, 25, 25, 25))
valid_set = ArrayIterator(X=X_test, y=y_test, nclass=2)
#tate=lt.plot(X_train[0, 12])
#plt.savefigure('data_img.png')
# setup weight initialization function
init = Gaussian(scale=0.01)
# discriminiator using convolution layers
lrelu = Rectlin(slope=0.1) # leaky relu for discriminator
# sigmoid = Logistic() # sigmoid activation function
conv1 = dict(init=init, batch_norm=False, activation=lrelu, bias=init)
conv2 = dict(init=init,
batch_norm=False,
filename = "splice_data_CAGT.csv"
names = ['class', 'C', 'A', 'G', 'T']
# Number of classes EI, IE and N
nclass = 3
# 20% of data used for validation
validation_size = 0.20
train_data, valid_data, train_label, valid_label = gene.load_data(
ip_file_path, filename, names, validation_size=0.20)
train_iter = ArrayIterator(train_data,
train_label,
nclass=nclass,
lshape=(1, 4),
name='train')
val_iter = ArrayIterator(valid_data,
valid_label,
nclass=nclass,
lshape=(1, 4),
name='valid')
# weight
w = Xavier()
# bias
b = Constant()
# setup model layers