def predict(filename):
with open(filename, 'rb') as f:
model = pickle.load(f)
print "Loading test images..."
labels = ImageIO().load_labels()
X,images = ImageIO().load_test_full()
print "Performing diversive augmentation and prediction..."
y_pred = diversive_augment(X, model)
print "Writing to file..."
df = DataFrame(np.round(y_pred, 8), index = images, columns = labels)
df.index.name = 'image'
df = df[header]
df.to_csv('out.csv')
print "Gzipping..."
call("gzip -c out.csv > out.csv.gz", shell=True)
print "Done! File saved to out.csv and out.csv.gz"
def compute_validation_predictions(model_id, validation_set):
d = importlib.import_module("nets.net_" + model_id)
model, X, y = d.define_net()
model.load_params_from(params.SAVE_URL + "/" + model_id + "/best_weights")
# Lower batch size since TTA multiplies batch size by 16
params.BATCH_SIZE = 32
io = ImageIO()
mean, std = io.load_mean_std()
# Read training labels for the keys
y = util.load_labels()
keys = y.index.values
model.batch_iterator_predict = TTABatchIterator(keys, params.BATCH_SIZE, std, mean, cv = True)
print "TTAs per image: %i, augmented batch size: %i" % (model.batch_iterator_predict.ttas, model.batch_iterator_predict.ttas * params.BATCH_SIZE)
padded_batches = ceil(validation_set.shape[0]/float(params.BATCH_SIZE))
pred = model.predict_proba(validation_set)
pred = pred.reshape(padded_batches, model.batch_iterator_predict.ttas, params.BATCH_SIZE)
pred = np.mean(pred, axis = 1)
pred = pred.reshape(padded_batches * params.BATCH_SIZE)
# Remove padded lines
pred = pred[:validation_set.shape[0]]
return pred
def fit(output):
X, y = ImageIO().load_train_full()
mean, std = ImageIO().load_mean_std()
with open(output, 'rb') as f:
net = pickle.load(f)
net.on_epoch_finished = [
AdjustVariable('update_learning_rate',
start=START_LEARNING_RATE *
10e-2), # Reduced learning rate for this step
EarlyStoppingNoValidation(training_loss_threshold=TRAINING_LOSS),
]
net.eval_size = None
net.fit(X, y)
with open(output + "_full", 'wb') as f:
pickle.dump(net, f, -1)
def define_net():
define_net_specific_parameters()
io = ImageIO()
# Read pandas csv labels
y = util.load_labels()
if params.SUBSET is not 0:
y = y[:params.SUBSET]
X = np.arange(y.shape[0])
mean, std = io.load_mean_std(circularized=params.CIRCULARIZED_MEAN_STD)
keys = y.index.values
if params.AUGMENT:
train_iterator = AugmentingParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
else:
train_iterator = ParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
test_iterator = ParallelBatchIterator(keys, params.BATCH_SIZE, std, mean, y_all = y)
if params.REGRESSION:
y = util.float32(y)
y = y[:, np.newaxis]
if 'gpu' in theano.config.device:
# Half of coma does not support cuDNN, check whether we can use it on this node
# If not, use cuda_convnet bindings
from theano.sandbox.cuda.dnn import dnn_available
if dnn_available():
from lasagne.layers import dnn
Conv2DLayer = dnn.Conv2DDNNLayer
MaxPool2DLayer = dnn.MaxPool2DDNNLayer
else:
from lasagne.layers import cuda_convnet
Conv2DLayer = cuda_convnet.Conv2DCCLayer
MaxPool2DLayer = cuda_convnet.MaxPool2DCCLayer
else:
Conv2DLayer = layers.Conv2DLayer
MaxPool2DLayer = layers.MaxPool2DLayer
Maxout = layers.pool.FeaturePoolLayer
net = NeuralNet(
layers=[
('input', layers.InputLayer),
('conv0', Conv2DLayer),
('pool0', MaxPool2DLayer),
('conv1', Conv2DLayer),
('pool1', MaxPool2DLayer),
('conv2', Conv2DLayer),
('pool2', MaxPool2DLayer),
('conv3', Conv2DLayer),
('pool3', MaxPool2DLayer),
('conv4', Conv2DLayer),
('pool4', MaxPool2DLayer),
('dropouthidden1', layers.DropoutLayer),
('hidden1', layers.DenseLayer),
('maxout1', Maxout),
('dropouthidden2', layers.DropoutLayer),
('hidden2', layers.DenseLayer),
('maxout2', Maxout),
('dropouthidden3', layers.DropoutLayer),
('output', layers.DenseLayer),
],
input_shape=(None, params.CHANNELS, params.PIXELS, params.PIXELS),
conv0_num_filters=32, conv0_filter_size=(5, 5), conv0_stride=(2, 2), pool0_pool_size=(2, 2), pool0_stride=(2, 2),
conv1_num_filters=64, conv1_filter_size=(5, 5), conv1_border_mode = 'same', pool1_pool_size=(2, 2), pool1_stride=(2, 2),
conv2_num_filters=128, conv2_filter_size=(3, 3), conv2_border_mode = 'same', pool2_pool_size=(2, 2), pool2_stride=(2, 2),
conv3_num_filters=192, conv3_filter_size=(3, 3), conv3_border_mode = 'same', pool3_pool_size=(2, 2), pool3_stride=(2, 2),
conv4_num_filters=256, conv4_filter_size=(3, 3), conv4_border_mode = 'same', pool4_pool_size=(2, 2), pool4_stride=(2, 2),
hidden1_num_units=1024,
hidden2_num_units=1024,
dropouthidden1_p=0.5,
dropouthidden2_p=0.5,
dropouthidden3_p=0.5,
maxout1_pool_size=2,
maxout2_pool_size=2,
output_num_units=1 if params.REGRESSION else 5,
output_nonlinearity=None if params.REGRESSION else nonlinearities.softmax,
update_learning_rate=theano.shared(util.float32(params.START_LEARNING_RATE)),
update_momentum=theano.shared(util.float32(params.MOMENTUM)),
custom_score=('kappa', quadratic_kappa),
regression=params.REGRESSION,
batch_iterator_train=train_iterator,
batch_iterator_test=test_iterator,
on_epoch_finished=[
AdjustVariable('update_learning_rate', start=params.START_LEARNING_RATE),
stats.Stat(),
ModelSaver()
],
max_epochs=500,
verbose=1,
# Only relevant when create_validation_split = True
eval_size=0.1,
# Need to specify splits manually like indicated below!
create_validation_split=params.SUBSET>0,
)
# It is recommended to use the same training/validation split every model for ensembling and threshold optimization
#
# To set specific training/validation split:
net.X_train = np.load(params.IMAGE_SOURCE + "/X_train.npy")
net.X_valid = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
net.y_train = np.load(params.IMAGE_SOURCE + "/y_train.npy")
net.y_valid = np.load(params.IMAGE_SOURCE + "/y_valid.npy")
return net, X, y
def predict(model_id, raw, validation, train, n_eyes, average_over_eyes):
params.DISABLE_CUDNN = True
params.MULTIPROCESS = False
d = importlib.import_module("nets.net_" + model_id)
model, X, y = d.define_net()
model.load_params_from(params.SAVE_URL + "/" + model_id + "/best_weights")
f = get_iter_func(model)
# Decrease batch size because TTA increases it 16-fold
# Uses too much memory otherwise
params.BATCH_SIZE = 8
io = ImageIO()
mean, std = io.load_mean_std()
if validation or train:
y = util.load_labels()
else:
y = util.load_sample_submission()
keys = y.index.values
tta_bi = TTABatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
cv=validation or train,
n_eyes=n_eyes)
print "TTAs per image: %i, augmented batch size: %i" % (
tta_bi.ttas, tta_bi.ttas * params.BATCH_SIZE * n_eyes)
if validation:
X_test = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
elif train:
X_test = np.load(params.IMAGE_SOURCE + "/X_train.npy")
else:
X_test = np.arange(y.shape[0])
padded_batches = ceil(X_test.shape[0] / float(params.BATCH_SIZE))
pred = get_activations(X_test, tta_bi, f)
concat_preds = []
for batch_pred in pred:
hidden = batch_pred[0]
output = batch_pred[1]
concat = np.concatenate([output, hidden], axis=1)
#if average_over_eyes:
#means = concat.reshape(concat.shape[0] / 2, 2, concat.shape[1])
#means = means.mean(axis = 1)
#means = np.repeat(means, 2, axis = 0)
concat_preds.append(concat)
pred = np.vstack(concat_preds)
output_units = pred.shape[1]
#pred = model.predict_proba(X_test)
pred = pred.reshape(padded_batches, tta_bi.ttas, params.BATCH_SIZE,
output_units)
pred = np.mean(pred, axis=1)
pred = pred.reshape(padded_batches * params.BATCH_SIZE, output_units)
# Remove padded lines
pred = pred[:X_test.shape[0]]
# Save unrounded
#y.loc[keys] = pred
if validation:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_validation.npy"
elif train:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_train.npy"
else:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_test.npy"
np.save(filename, pred)
#y.to_csv(filename)
print "Saved raw predictions to " + filename
if not raw and not validation and not train:
W = np.load(params.SAVE_URL + "/" + model_id +
"/optimal_thresholds.npy")
pred = weighted_round(pred, W)
pred = pred[:, np.newaxis] # add axis for pd compatability
hist, _ = np.histogram(pred, bins=5)
print "Distribution over class predictions on test set: ", hist / float(
y.shape[0])
y.loc[keys] = pred
y.to_csv(params.SAVE_URL + "/" + model_id + "/submission.csv")
print "Gzipping..."
if not params.ON_COMA:
call("gzip -c " + params.SAVE_URL + "/" + model_id +
"/submission.csv > " + params.SAVE_URL + "/" + model_id +
"/submission.csv.gz",
shell=True)
print "Done! File saved to models/" + model_id + "/submission.csv"
def define_net():
define_net_specific_parameters()
io = ImageIO()
# Read pandas csv labels
y = util.load_labels()
if params.SUBSET is not 0:
y = y[:params.SUBSET]
X = np.arange(y.shape[0])
mean, std = io.load_mean_std(circularized=params.CIRCULARIZED_MEAN_STD)
keys = y.index.values
if params.AUGMENT:
train_iterator = AugmentingParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
else:
train_iterator = ParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
test_iterator = ParallelBatchIterator(keys,
params.BATCH_SIZE,
std,
mean,
y_all=y)
if params.REGRESSION:
y = util.float32(y)
y = y[:, np.newaxis]
if 'gpu' in theano.config.device:
# Half of coma does not support cuDNN, check whether we can use it on this node
# If not, use cuda_convnet bindings
from theano.sandbox.cuda.dnn import dnn_available
if dnn_available() and not params.DISABLE_CUDNN:
from lasagne.layers import dnn
Conv2DLayer = dnn.Conv2DDNNLayer
MaxPool2DLayer = dnn.MaxPool2DDNNLayer
else:
from lasagne.layers import cuda_convnet
Conv2DLayer = cuda_convnet.Conv2DCCLayer
MaxPool2DLayer = cuda_convnet.MaxPool2DCCLayer
else:
Conv2DLayer = layers.Conv2DLayer
MaxPool2DLayer = layers.MaxPool2DLayer
Maxout = layers.pool.FeaturePoolLayer
net = NeuralNet(
layers=[
('input', layers.InputLayer),
('conv0', Conv2DLayer),
('pool0', MaxPool2DLayer),
('conv1', Conv2DLayer),
('pool1', MaxPool2DLayer),
('conv2', Conv2DLayer),
('pool2', MaxPool2DLayer),
('conv3', Conv2DLayer),
('pool3', MaxPool2DLayer),
('conv4', Conv2DLayer),
('pool4', MaxPool2DLayer),
('dropouthidden1', layers.DropoutLayer),
('hidden1', layers.DenseLayer),
('maxout1', Maxout),
('dropouthidden2', layers.DropoutLayer),
('hidden2', layers.DenseLayer),
('maxout2', Maxout),
('dropouthidden3', layers.DropoutLayer),
('output', layers.DenseLayer),
],
input_shape=(None, params.CHANNELS, params.PIXELS, params.PIXELS),
conv0_num_filters=32,
conv0_filter_size=(5, 5),
conv0_stride=(2, 2),
pool0_pool_size=(2, 2),
pool0_stride=(2, 2),
conv1_num_filters=64,
conv1_filter_size=(3, 3),
conv1_border_mode='same',
pool1_pool_size=(2, 2),
pool1_stride=(2, 2),
conv2_num_filters=128,
conv2_filter_size=(3, 3),
conv2_border_mode='same',
pool2_pool_size=(2, 2),
pool2_stride=(2, 2),
conv3_num_filters=192,
conv3_filter_size=(3, 3),
conv3_border_mode='same',
pool3_pool_size=(2, 2),
pool3_stride=(2, 2),
conv4_num_filters=256,
conv4_filter_size=(3, 3),
conv4_border_mode='same',
pool4_pool_size=(2, 2),
pool4_stride=(2, 2),
hidden1_num_units=1024,
hidden2_num_units=1024,
dropouthidden1_p=0.5,
dropouthidden2_p=0.5,
dropouthidden3_p=0.5,
maxout1_pool_size=2,
maxout2_pool_size=2,
output_num_units=1 if params.REGRESSION else 5,
output_nonlinearity=None
if params.REGRESSION else nonlinearities.softmax,
update_learning_rate=theano.shared(
util.float32(params.START_LEARNING_RATE)),
update_momentum=theano.shared(util.float32(params.MOMENTUM)),
custom_score=('kappa', quadratic_kappa),
regression=params.REGRESSION,
batch_iterator_train=train_iterator,
batch_iterator_test=test_iterator,
on_epoch_finished=[
AdjustVariable('update_learning_rate',
start=params.START_LEARNING_RATE),
stats.Stat(),
ModelSaver()
],
max_epochs=500,
verbose=1,
# Only relevant when create_validation_split = True
eval_size=0.1,
# Need to specify splits manually like indicated below!
create_validation_split=params.SUBSET > 0,
)
# It is recommended to use the same training/validation split every model for ensembling and threshold optimization
#
# To set specific training/validation split:
net.X_train = np.load(params.IMAGE_SOURCE + "/X_train.npy")
net.X_valid = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
net.y_train = np.load(params.IMAGE_SOURCE + "/y_train.npy")
net.y_valid = np.load(params.IMAGE_SOURCE + "/y_valid.npy")
return net, X, y
def predict(model_id, raw, validation, train, n_eyes, average_over_eyes):
params.DISABLE_CUDNN = True
params.MULTIPROCESS = False
d = importlib.import_module("nets.net_" + model_id)
model, X, y = d.define_net()
model.load_params_from(params.SAVE_URL + "/" + model_id + "/best_weights")
f = get_iter_func(model)
# Decrease batch size because TTA increases it 16-fold
# Uses too much memory otherwise
params.BATCH_SIZE = 8
io = ImageIO()
mean, std = io.load_mean_std()
if validation or train:
y = util.load_labels()
else:
y = util.load_sample_submission()
keys = y.index.values
tta_bi = TTABatchIterator(keys, params.BATCH_SIZE, std, mean, cv = validation or train, n_eyes = n_eyes)
print "TTAs per image: %i, augmented batch size: %i" % (tta_bi.ttas, tta_bi.ttas * params.BATCH_SIZE * n_eyes)
if validation:
X_test = np.load(params.IMAGE_SOURCE + "/X_valid.npy")
elif train:
X_test = np.load(params.IMAGE_SOURCE + "/X_train.npy")
else:
X_test = np.arange(y.shape[0])
padded_batches = ceil(X_test.shape[0]/float(params.BATCH_SIZE))
pred = get_activations(X_test, tta_bi, f)
concat_preds = []
for batch_pred in pred:
hidden = batch_pred[0]
output = batch_pred[1]
concat = np.concatenate([output, hidden], axis = 1)
#if average_over_eyes:
#means = concat.reshape(concat.shape[0] / 2, 2, concat.shape[1])
#means = means.mean(axis = 1)
#means = np.repeat(means, 2, axis = 0)
concat_preds.append(concat)
pred = np.vstack(concat_preds)
output_units = pred.shape[1]
#pred = model.predict_proba(X_test)
pred = pred.reshape(padded_batches, tta_bi.ttas, params.BATCH_SIZE, output_units)
pred = np.mean(pred, axis = 1)
pred = pred.reshape(padded_batches * params.BATCH_SIZE, output_units)
# Remove padded lines
pred = pred[:X_test.shape[0]]
# Save unrounded
#y.loc[keys] = pred
if validation:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_validation.npy"
elif train:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_train.npy"
else:
filename = params.SAVE_URL + "/" + model_id + "/raw_predictions_test.npy"
np.save(filename, pred)
#y.to_csv(filename)
print "Saved raw predictions to " + filename
if not raw and not validation and not train:
W = np.load(params.SAVE_URL + "/" + model_id + "/optimal_thresholds.npy")
pred = weighted_round(pred, W)
pred = pred[:, np.newaxis] # add axis for pd compatability
hist, _ = np.histogram(pred, bins=5)
print "Distribution over class predictions on test set: ", hist / float(y.shape[0])
y.loc[keys] = pred
y.to_csv(params.SAVE_URL + "/" + model_id + "/submission.csv")
print "Gzipping..."
if not params.ON_COMA:
call("gzip -c " + params.SAVE_URL + "/" + model_id + "/submission.csv > " + params.SAVE_URL + "/" + model_id + "/submission.csv.gz", shell=True)
print "Done! File saved to models/" + model_id + "/submission.csv"
