def save_planet(logger, name, epochs, size, batch_size, treshold, iterations,
TTA):
start_time = time.time()
temp_training_dir, temp_validation_dir = du.make_temp_dirs(logger.ts, name)
du.fill_temp_training_folder(temp_training_dir)
du.move_to_validation_folder(temp_training_dir, temp_validation_dir)
train_directory = os.path.split(temp_training_dir)[0]
validation_directory = os.path.split(temp_validation_dir)[0]
test_directory = '../data/interim/consensus_test/'
# -------load metadata---------- #
labels, df_train, df_test, label_map, train_mapping, validation_mapping, y_train, y_valid = fu.load_metadata(
temp_training_dir, temp_validation_dir)
n_train_files = len(os.listdir(os.path.join(train_directory, 'train')))
n_validation_files = len(
os.listdir(os.path.join(validation_directory, 'validation')))
n_test_files = len(os.listdir(os.path.join(test_directory, 'test')))
# Generators - with and without data augmentation
gen_no_augmentation = extended_generator.ImageDataGenerator(rescale=1. /
255)
gen_augmentation = extended_generator.ImageDataGenerator(
rotation_range=0,
width_shift_range=0.05,
height_shift_range=0.05,
horizontal_flip=True,
vertical_flip=True,
rescale=1. / 255)
# Training data: with augmentation - with labels
training_generator = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode='multilabel',
multilabel_classes=train_mapping,
n_class=17,
batch_size=batch_size)
# Validation data: without augmentation - with labels
validation_generator = gen_no_augmentation.flow_from_directory(
validation_directory,
target_size=(size, size),
class_mode='multilabel',
multilabel_classes=validation_mapping,
n_class=17,
batch_size=batch_size,
shuffle=False)
# Training data: with TTA - no labels
# This one has to be calles AFTER the validation data has been moved back!
# Otherwise it doesn't know the correct amount of images.
print('Saving bottleneck features...')
save_bottlebeck_features(size, gen_no_augmentation, train_directory,
validation_directory, train_mapping,
validation_mapping, name, logger.ts)
print('Done')
print('Training top model...')
train_shape = train_top_model(size, train_directory, validation_directory,
train_mapping, validation_mapping, name,
logger.ts, batch_size)
print('Done')
print('Finetuning VGG...')
model, optimizer = reconstruct_VGG(
'../models/top_model_{}_{}.h5'.format(logger.ts, name), size,
train_shape, logger.ts, name)
# Finetune the model
callbacks = [
EarlyStopping(monitor='val_loss', patience=4, verbose=1),
ModelCheckpoint('../models/VGG_{}_{}.h5'.format(logger.ts, name),
monitor='val_loss',
save_best_only=True,
verbose=1),
ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=2,
cooldown=2,
verbose=1)
]
model.fit_generator(generator=training_generator,
steps_per_epoch=n_train_files / batch_size,
epochs=epochs,
callbacks=callbacks,
validation_data=(validation_generator),
validation_steps=n_validation_files / batch_size)
print('Done.')
# Load best model
model.load_weights('../models/VGG_{}_{}.h5'.format(logger.ts, name))
model.compile(loss='binary_crossentropy',
optimizer=optimizer,
metrics=['accuracy'])
# --------move back validation data--------- #
du.empty_validation_folder(temp_training_dir, temp_validation_dir)
print('Remapping labels...')
train_files = [f.split('.')[0] for f in os.listdir(temp_training_dir)]
train_labels = [
df_train.iloc[np.where(
df_train.image_name.values == train_file)].tags.values[0]
for train_file in train_files
]
y_train = fu.binarize(train_labels, label_map)
print('Done.')
n_train_files = len(os.listdir(temp_training_dir))
# -------Search for best thresholds-------- #
# Predict full training data. With TTA to make predictions stable!
print('TTA ({} loops)...'.format(TTA))
predictions_train = []
for i in range(TTA):
training_generator_TTA = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
predictions_train.append(
model.predict_generator(generator=training_generator_TTA,
steps=n_train_files / batch_size,
verbose=1))
print('Done.')
# Take the average predicted probabilities
p_train = np.mean(predictions_train, axis=0)
print(p_train.shape)
print('Finding thresholds...')
from sklearn.metrics import fbeta_score
best_bac, score = fo.optimize_BAC(y_train, p_train, num_tries=iterations)
score = str(np.round(score, 3))
score_nothresh = fbeta_score(y_train, (p_train > 0.2).astype(int),
beta=2,
average='samples')
print('Score on training data without optimization: {}'.format(
score_nothresh))
print('Score on training data with thresholds bac: {}'.format(score))
# -------Store-------- #
if float(score) > treshold:
print('Test set TTA ({} loops)...'.format(TTA))
predictions_test = []
for i in range(TTA):
# Test data: with TTA - no labels
test_generator = gen_augmentation.flow_from_directory(
test_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
predictions_test.append(
model.predict_generator(generator=test_generator,
steps=n_test_files / batch_size,
verbose=1))
print('Done')
p_test = np.mean(predictions_test, axis=0)
p_test_binary = (p_test > best_bac).astype(int)
# Convert binary predictions to label strings - define a mapping to the file names
preds = [
' '.join(np.array(labels)[pred_row == 1])
for pred_row in p_test_binary
]
test_mapping = dict(
zip([
f.split('/')[1].split('.')[0] for f in test_generator.filenames
], preds))
# Map the predictions to filenames in df_test
predictions_df = pd.DataFrame({
'image_name': df_test.image_name,
'tags': df_test.image_name
})
predictions_df['tags'] = predictions_df['tags'].map(test_mapping)
# Save predictions without consensus predictions
predictions_df.to_csv('../logs/predictions/VGG_{}_{}_{}.csv'.format(
logger.ts, name, score),
index=False)
else:
logger.log_event('Low score - not storing anything.')
# Remove temp folders
du.remove_temp_dirs(logger.ts, name)
elapsed_time = time.time() - start_time
print('Elapsed time: {} minutes'.format(np.round(elapsed_time / 60, 2)))
print('Done.')
start_time = time.time()
ts = start_time
temp_training_dir, temp_validation_dir = du.make_temp_dirs(ts, name)
du.empty_validation_folder(temp_training_dir, temp_validation_dir)
du.fill_temp_training_folder(temp_training_dir)
du.move_to_validation_folder(temp_training_dir, temp_validation_dir)
# ------ call data generators ------#
train_directory = os.path.split(temp_training_dir)[0]
validation_directory = os.path.split(temp_validation_dir)[0]
test_directory = '../data/interim/consensus_test/'
# -------load metadata---------- #
labels, df_train, df_test, label_map, train_mapping, validation_mapping, y_train, y_valid = fu.load_metadata(temp_training_dir, temp_validation_dir)
n_train_files = len(os.listdir(os.path.join(train_directory, 'train')))
n_validation_files = len(os.listdir(os.path.join(validation_directory, 'validation')))
n_test_files = len(os.listdir(os.path.join(test_directory, 'test')))
# Generators - with and without data augmentation
gen_no_augmentation = extended_generator.ImageDataGenerator(rescale=1./255)
gen_augmentation = extended_generator.ImageDataGenerator(rotation_range=0, width_shift_range=0.05, height_shift_range=0.05,
horizontal_flip=True, vertical_flip=True, rescale=1./255)
# Training data: with augmentation - with labels
training_generator = gen_augmentation.flow_from_directory(train_directory, target_size=(size,size),
class_mode='multilabel', multilabel_classes=train_mapping, n_class=17, batch_size=batch_size)
# Validation data: without augmentation - with labels
def save_planet(logger,
name,
epochs,
size,
batch_size,
learning_rate,
treshold,
TTA,
debug=False):
start_time = time.time()
ts = logger.ts
temp_training_dir, temp_validation_dir = du.make_temp_dirs(ts, name)
du.fill_temp_training_folder(temp_training_dir)
du.move_to_validation_folder(temp_training_dir, temp_validation_dir)
# ------ call data generators ------#
train_directory = os.path.split(temp_training_dir)[0]
validation_directory = os.path.split(temp_validation_dir)[0]
test_directory = '../data/interim/consensus_test/'
# -------load metadata---------- #
labels, df_train, df_test, label_map, train_mapping, validation_mapping, y_train, y_valid = fu.load_metadata(
temp_training_dir, temp_validation_dir)
n_train_files = len(os.listdir(os.path.join(train_directory, 'train')))
n_validation_files = len(
os.listdir(os.path.join(validation_directory, 'validation')))
n_test_files = len(os.listdir(os.path.join(test_directory, 'test')))
# -------Convert training and validation labels into the matrix format for GFM---------- #
Y_train = GFM.matrix_Y(y_train)
Y_valid = GFM.matrix_Y(y_valid)
# Generate 17 output vectors for training and validation data
outputs_train = []
outputs_valid = []
field_size = []
enc = encoder.fit(
np.arange(0, 10).reshape(-1, 1)
) # fit the encoder on here and not per label!!! to make sure that every possible class is encoded
for i in range(Y_train.shape[1]):
# concatenate train and validation data to fit the encoder
Y_train_i = enc.transform(Y_train[:, i].reshape(-1, 1))
Y_valid_i = enc.transform(Y_valid[:, i].reshape(-1, 1))
outputs_train.append(Y_train_i)
outputs_valid.append(Y_valid_i)
field_size.append(Y_train_i.shape[1])
print('Field sizes: {}'.format(field_size))
# Put the outputs in a list of lists of arrays
# (maybe making hte output_train and output_valid lists is redundant?)
output_fields_train = []
output_fields_validation = []
for i in range(n_train_files):
output_fields_train.append(
[output_field[i, :] for output_field in outputs_train])
for i in range(n_validation_files):
output_fields_validation.append(
[output_field[i, :] for output_field in outputs_valid])
# Redefine the labels mappings to the elements of Y_train and Y_valid required for the generators
# Be careful with the ordering!!!
# The dicts should have filenames as keys and lists of arrays as values
print('Redefine label dicts to the elements of matrices P...')
train_files = [f.split('.')[0] for f in os.listdir(temp_training_dir)]
val_files = [f.split('.')[0] for f in os.listdir(temp_validation_dir)]
train_mapping = dict(
zip(['train/' + t + '.jpg' for t in train_files], output_fields_train))
validation_mapping = dict(
zip(['validation/' + t + '.jpg' for t in val_files],
output_fields_validation))
print('Done.')
# Generators - with and without data augmentation
gen_no_augmentation = extended_generator_GFM.ImageDataGenerator(
rescale=1. / 255)
gen_augmentation = extended_generator_GFM.ImageDataGenerator(
rotation_range=0,
width_shift_range=0.05,
height_shift_range=0.05,
horizontal_flip=True,
vertical_flip=True,
rescale=1. / 255)
# Training data: with augmentation - with labels
training_generator = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode='GFM',
multilabel_classes=train_mapping,
n_class=17,
batch_size=batch_size,
field_sizes=field_size)
# Validation data: without augmentation - with labels
validation_generator = gen_no_augmentation.flow_from_directory(
validation_directory,
target_size=(size, size),
class_mode='GFM',
multilabel_classes=validation_mapping,
n_class=17,
batch_size=batch_size,
shuffle=False,
field_sizes=field_size)
# --------load model--------- #
print("Initializing model...")
if debug:
architecture = m.SimpleCNN_joint_GFM(size, field_size)
else:
architecture = m.SimpleNet64_joint_GFM(size, field_size)
model = Model(inputs=architecture.input, outputs=architecture.output)
def lr_schedule(epoch):
"""Learning rate scheduler"""
return learning_rate * (0.1**int(epoch / 10))
sgd = SGD(lr=learning_rate, decay=1e-6, momentum=0.9, nesterov=True)
weights = [1] * 17 # put equal weights on all loss fields
model.compile(loss='binary_crossentropy',
optimizer=sgd,
loss_weights=weights)
callbacks = [
EarlyStopping(monitor='val_loss', patience=4, verbose=1),
ModelCheckpoint('../models/GFM_{}_{}.h5'.format(logger.ts, name),
monitor='val_loss',
save_best_only=True,
verbose=1),
LearningRateScheduler(lr_schedule)
]
# --------training model--------- #
history = model.fit_generator(generator=training_generator,
steps_per_epoch=n_train_files / batch_size,
epochs=epochs,
verbose=1,
callbacks=callbacks,
validation_data=(validation_generator),
validation_steps=n_validation_files /
batch_size)
# Load best model
model.load_weights('../models/GFM_{}_{}.h5'.format(logger.ts, name))
model.compile(loss='binary_crossentropy', optimizer='adam')
# Make predictions for training, for validation and for data. With TTA!
# Call generators inside the loop!
print('TTA ({} loops)...'.format(TTA))
predictions_train = []
predictions_valid = []
predictions_test = []
for i in range(TTA):
training_generator_TTA = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
validation_generator_TTA = gen_augmentation.flow_from_directory(
validation_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
test_generator_TTA = gen_augmentation.flow_from_directory(
test_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
predictions_train.append(
model.predict_generator(generator=training_generator_TTA,
steps=n_train_files / batch_size,
verbose=1))
predictions_valid.append(
model.predict_generator(generator=validation_generator_TTA,
steps=n_validation_files / batch_size,
verbose=1))
predictions_test.append(
model.predict_generator(generator=test_generator_TTA,
steps=n_test_files / batch_size,
verbose=1))
print('Done.')
# Average TTA predictions - bug here
def average_TTA(predictions, TTA):
"""Average TTA predictions for GFM output
Input
----
predictions: list of len TTA
"""
return ([
np.mean([np.array(predictions[i][j]) for i in range(TTA)], axis=0)
for j in range(17)
])
predictions_train_avg = average_TTA(predictions_train, TTA)
predictions_valid_avg = average_TTA(predictions_valid, TTA)
predictions_test_avg = average_TTA(predictions_test, TTA)
# Fill up the predictions so that they have length 17
predictions_train_filled = []
predictions_valid_filled = []
predictions_test_filled = []
for pred in predictions_train_avg:
predictions_train_filled.append(GFM.complete_pred(pred[:, 1:], 17))
for pred in predictions_valid_avg:
predictions_valid_filled.append(GFM.complete_pred(pred[:, 1:], 17))
for pred in predictions_test_avg:
predictions_test_filled.append(GFM.complete_pred(pred[:, 1:], 17))
W = GFM.matrix_W_F2(beta=2, n_labels=17)
(optimal_predictions_train, E_F_train) = GFM.GFM(17, n_train_files,
predictions_train_filled,
W)
(optimal_predictions_valid, E_F_valid) = GFM.GFM(17, n_validation_files,
predictions_valid_filled,
W)
(optimal_predictions_test, E_F_test) = GFM.GFM(17, n_test_files,
predictions_test_filled, W)
# Store the predictions for the matrix P and the F-optimal predictions to analyze them
# Also store y_train and the labels
import pickle
with open('../logs/pickles/{}_{}_P_train'.format(ts, name), 'wb') as fp:
pickle.dump(predictions_train_filled, fp)
with open('../logs/pickles/{}_{}_p_train'.format(ts, name), 'wb') as fp:
pickle.dump(optimal_predictions_train, fp)
with open('../logs/pickles/{}_{}_y_train'.format(ts, name), 'wb') as fp:
pickle.dump(y_train, fp)
with open('../logs/pickles/{}_{}_filenames'.format(ts, name), 'wb') as fp:
pickle.dump(training_generator_TTA.filenames, fp)
score_GFM_train = fbeta_score(y_train,
optimal_predictions_train,
beta=2,
average='samples')
print(
'F_2 score on the training data with GFM: {}'.format(score_GFM_train))
score_GFM_valid = fbeta_score(y_valid,
optimal_predictions_valid,
beta=2,
average='samples')
print('F_2 score on the validation data with GFM: {}'.format(
score_GFM_valid))
# -------Store-------- #
if float(score_GFM_valid) > treshold:
# Convert binary predictions to label strings - define a mapping to the file names
preds = [
' '.join(np.array(labels)[pred_row == 1])
for pred_row in optimal_predictions_test
]
test_mapping = dict(
zip([
f.split('/')[1].split('.')[0]
for f in test_generator_TTA.filenames
], preds))
# Map the predictions to filenames in df_test
predictions_df = pd.DataFrame({
'image_name': df_test.image_name,
'tags': df_test.image_name
})
predictions_df['tags'] = predictions_df['tags'].map(test_mapping)
# Save predictions without consensus predictions
predictions_df.to_csv('../logs/predictions/GFM_{}_{}_{}.csv'.format(
ts, name, score_GFM_valid),
index=False)
else:
logger.log_event('Low score - not storing anything.')
def save_planet(logger, name, epochs, size, batch_size, learning_rate,
treshold, iterations, TTA, optimizer, debug=False):
start_time = time.time()
ts = logger.ts
temp_training_dir, temp_validation_dir = du.make_temp_dirs(ts, name)
du.fill_temp_training_folder(temp_training_dir)
du.move_to_validation_folder(temp_training_dir, temp_validation_dir)
# ------ call data generators ------#
train_directory = os.path.split(temp_training_dir)[0]
validation_directory = os.path.split(temp_validation_dir)[0]
test_directory = '../data/interim/consensus_test/'
# -------load metadata---------- #
labels, df_train, df_test, label_map, train_mapping, validation_mapping, y_train, y_valid = fu.load_metadata(temp_training_dir, temp_validation_dir)
n_train_files = len(os.listdir(os.path.join(train_directory, 'train')))
n_validation_files = len(os.listdir(os.path.join(validation_directory, 'validation')))
n_test_files = len(os.listdir(os.path.join(test_directory, 'test')))
# Generators - with and without data augmentation
gen_no_augmentation = extended_generator.ImageDataGenerator(rescale=1./255)
gen_augmentation = extended_generator.ImageDataGenerator(rotation_range=0, width_shift_range=0.05, height_shift_range=0.05,
horizontal_flip=True, vertical_flip=True, rescale=1./255)
# Training data: with augmentation - with labels
training_generator = gen_augmentation.flow_from_directory(train_directory, target_size=(size,size),
class_mode='multilabel', multilabel_classes=train_mapping, n_class=17, batch_size=batch_size)
# Validation data: without augmentation - with labels
validation_generator = gen_no_augmentation.flow_from_directory(validation_directory, target_size=(size,size),
class_mode='multilabel', multilabel_classes=validation_mapping, n_class=17, batch_size=batch_size, shuffle=False)
# Training data: with TTA - no labels
# This one has to be calles AFTER the validation data has been moved back!
# Otherwise it doesn't know the correct amount of images.
# --------load model--------- #
logger.log_event("Initializing model...")
if debug:
architecture = m.SimpleCNN(size, output_size=17)
else:
architecture = m.SimpleNet64_2(size, output_size=17)
model = Model(inputs=architecture.input, outputs=architecture.output)
def lr_schedule(epoch):
"""Learning rate scheduler"""
return learning_rate * (0.1 ** int(epoch / 10))
if optimizer == 'adam':
optimizer = Adam()
elif optimizer == 'sgd':
optimizer = SGD(lr=learning_rate, decay=1e-6, momentum=0.9, nesterov=True)
model.compile(loss='binary_crossentropy', optimizer=optimizer, metrics=['accuracy'])
callbacks = [EarlyStopping(monitor='val_loss', patience=4, verbose=1),
ModelCheckpoint('../models/{}_{}.h5'.format(logger.ts, name),
monitor='val_loss', save_best_only=True, verbose=1),
LearningRateScheduler(lr_schedule)]
# --------training model--------- #
history = model.fit_generator(generator=training_generator, steps_per_epoch=n_train_files/batch_size,epochs=epochs, verbose=1,
callbacks=callbacks, validation_data=(validation_generator), validation_steps=n_validation_files/batch_size)
# Load best model
model.load_weights('../models/{}_{}.h5'.format(logger.ts, name))
model.compile(loss='binary_crossentropy', optimizer=optimizer, metrics=['accuracy'])
# --------move back validation data--------- #
du.empty_validation_folder(temp_training_dir, temp_validation_dir)
print('Remapping labels...')
train_files = [f.split('.')[0] for f in os.listdir(temp_training_dir)]
train_labels = [df_train.iloc[np.where(df_train.image_name.values == train_file)].tags.values[0] for train_file in train_files]
y_train = fu.binarize(train_labels, label_map)
print('Done.')
n_train_files = len(os.listdir(temp_training_dir))
# Finetune model on full data with 100x smaller lr for 5 epochs
#model.compile(loss='binary_crossentropy', optimizer=Adam(lr=0.0001, decay=0.5), metrics=['accuracy'])
#model.fit_generator(generator=training_generator, steps_per_epoch=n_train_files/batch_size,epochs=5, verbose=1)
#model.save('../models/{}_{}_finetuned.h5'.format(logger.ts, name))
# -------Search for best thresholds-------- #
# Predict full training data. With TTA to make predictions stable!
print('TTA ({} loops)...'.format(TTA))
predictions_train = []
for i in range(TTA):
training_generator_TTA = gen_augmentation.flow_from_directory(train_directory, target_size=(size,size),
class_mode=None, batch_size=batch_size, shuffle=False)
predictions_train.append(model.predict_generator(generator=training_generator_TTA, steps=n_train_files/batch_size, verbose=1))
print('Done.')
# Take the average predicted probabilities
p_train = np.mean(predictions_train, axis=0)
print(p_train.shape)
print('Finding thresholds...')
from sklearn.metrics import fbeta_score
best_bac, score = fo.optimize_BAC(y_train, p_train, num_tries=iterations)
score = str(np.round(score,3))
score_nothresh = fbeta_score(y_train, (p_train > 0.2).astype(int), beta=2, average='samples')
print('Score on training data without optimization: {}'.format(score_nothresh))
print('Score on training data with thresholds bac: {}'.format(score))
# -------Store-------- #
if float(score) > treshold:
print('Test set TTA ({} loops)...'.format(TTA))
predictions_test = []
for i in range(TTA):
# Test data: with TTA - no labels
test_generator = gen_augmentation.flow_from_directory(test_directory, target_size=(size, size),
class_mode=None, batch_size=batch_size, shuffle=False)
predictions_test.append(model.predict_generator(generator=test_generator, steps=n_test_files/batch_size, verbose=1))
print('Done')
p_test = np.mean(predictions_test, axis=0)
p_test_binary = (p_test > best_bac).astype(int)
# Convert binary predictions to label strings - define a mapping to the file names
preds = [' '.join(np.array(labels)[pred_row == 1]) for pred_row in p_test_binary]
test_mapping = dict(zip([f.split('/')[1].split('.')[0] for f in test_generator.filenames], preds))
# Map the predictions to filenames in df_test
predictions_df = pd.DataFrame({'image_name': df_test.image_name, 'tags': df_test.image_name})
predictions_df['tags'] = predictions_df['tags'].map(test_mapping)
# Save predictions without consensus predictions
predictions_df.to_csv('../logs/predictions/{}_{}_{}.csv'.format(logger.ts, name, score), index=False)
# Save training history and model architecture
pd.DataFrame(history.history).to_pickle('../models/{}_{}_{}.pkl'.format(logger.ts, name, score))
with open('../models/{}_{}_{}_architecture.json'.format(logger.ts, name, score), 'w') as json_file:
json_file.write(model.to_json())
else:
logger.log_event('Low score - not storing anything.')
# Remove temp folders
du.remove_temp_dirs(ts, name)
elapsed_time = time.time() - start_time
print('Elapsed time: {} minutes'.format(np.round(elapsed_time/60, 2)))
import features.feature_utils as fu
import models.model_utils as mu
import models.models as m
import models.F_optimizers as fo
import plots.plot_utils as pu
import log_utils as lu
# Import extended datagenerator
# Source: https://gist.github.com/jandremarais/6bf673c76203f612f5ab2981430eb2ef
import extended_generator
size = 256
batch_size = 32
# -------load metadata---------- #
labels, df_train, df_test, train_mapping, y_train = fu.load_metadata(
consensus_data=True)
# ------ call data generators ------#
gen_train = extended_generator.ImageDataGenerator(rotation_range=10,
width_shift_range=0.05,
height_shift_range=0.05,
fill_mode='reflect',
horizontal_flip=True,
vertical_flip=True,
rescale=1. / 255)
train_directory = '../data/interim/consensus_train/'
n_train_files = len(os.listdir('../data/interim/consensus_train/train'))
train_generator = gen_train.flow_from_directory(
train_directory,
target_size=(size, size),
def save_planet(logger,
name,
epochs,
size,
batch_size,
treshold,
TTA,
nodes,
finetune,
load_weights,
optimizer,
debug=False):
ts = logger.ts
start_time = time.time()
# --- Preprocessing --- #
# Make temporary directories, fill with training and validation data
temp_training_dir, temp_validation_dir = du.make_temp_dirs(logger.ts, name)
du.fill_temp_training_folder(temp_training_dir)
du.move_to_validation_folder(temp_training_dir, temp_validation_dir)
# High level directories required for generators
train_directory = os.path.split(temp_training_dir)[0]
validation_directory = os.path.split(temp_validation_dir)[0]
test_directory = '../data/interim/consensus_test/'
n_train_files = len(os.listdir(temp_training_dir))
n_validation_files = len(os.listdir(temp_validation_dir))
n_test_files = len(os.listdir(os.path.join(test_directory, 'test')))
# Load required metadata
labels, df_train, df_test, label_map, train_mapping, validation_mapping, y_train, y_valid = fu.load_metadata(
temp_training_dir, temp_validation_dir)
#Convert training and validation labels into the matrix format for GFM method
Y_train = GFM.matrix_Y(y_train)
Y_valid = GFM.matrix_Y(y_valid)
# Generate 17 output vectors for training and validation data
outputs_train = []
outputs_valid = []
field_size = []
enc = encoder.fit(
np.arange(0, 10).reshape(-1, 1)
) # fit the encoder on here and not per label!!! to make sure that every possible class is encoded
for i in range(Y_train.shape[1]):
Y_train_i = enc.transform(Y_train[:, i].reshape(-1, 1))
Y_valid_i = enc.transform(Y_valid[:, i].reshape(-1, 1))
outputs_train.append(Y_train_i)
outputs_valid.append(Y_valid_i)
field_size.append(Y_train_i.shape[1])
print('Field sizes: {}'.format(field_size)
) # Same size everywhere because of fitting prior to for loop
# Put the outputs in a list of lists of arrays
# (maybe making the output_train and output_valid lists is redundant?)
output_fields_train = []
output_fields_validation = []
for i in range(n_train_files):
output_fields_train.append(
[output_field[i, :] for output_field in outputs_train])
for i in range(n_validation_files):
output_fields_validation.append(
[output_field[i, :] for output_field in outputs_valid])
# Train and validation mappings required for the generators to yield the labels in the GFM format
# The dicts should have filenames as keys and lists of arrays as values
print('Redefine label dicts to the elements of matrices P...')
train_files = [f.split('.')[0] for f in os.listdir(temp_training_dir)]
val_files = [f.split('.')[0] for f in os.listdir(temp_validation_dir)]
train_mapping = dict(
zip(['train/' + t + '.jpg' for t in train_files], output_fields_train))
validation_mapping = dict(
zip(['validation/' + t + '.jpg' for t in val_files],
output_fields_validation))
print('Done.')
# Generators - with and without data augmentation
gen_no_augmentation = extended_generator_GFM.ImageDataGenerator(
rescale=1. / 255)
gen_augmentation = extended_generator_GFM.ImageDataGenerator(
rotation_range=0,
width_shift_range=0.05,
height_shift_range=0.05,
horizontal_flip=True,
vertical_flip=True,
rescale=1. / 255,
fill_mode='reflect')
# Training data: with augmentation - with labels
training_generator = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode='GFM',
multilabel_classes=train_mapping,
n_class=17,
batch_size=batch_size,
field_sizes=field_size)
# Validation data: without augmentation - with labels
validation_generator = gen_no_augmentation.flow_from_directory(
validation_directory,
target_size=(size, size),
class_mode='GFM',
multilabel_classes=validation_mapping,
n_class=17,
batch_size=batch_size,
shuffle=False,
field_sizes=field_size)
if debug:
print('Reading previously stored features...')
if size == 48:
features_train = np.load(
'../models/GFM_VGG/debug_features_train_48.npy')
features_valid = np.load(
'../models/GFM_VGG/debug_features_valid_48.npy')
features_test = np.load(
'../models/GFM_VGG/debug_features_test_48.npy')
elif size == 128:
features_train = np.load(
'../models/GFM_VGG/debug_features_train_128.npy')
features_valid = np.load(
'../models/GFM_VGG/debug_features_valid_128.npy')
features_test = np.load(
'../models/GFM_VGG/debug_features_test_128.npy')
else:
print('Producing bottleneck features...')
save_bottlebeck_features(size, gen_no_augmentation, train_directory,
validation_directory, test_directory, name,
logger.ts)
print('Saving bottleneck features...')
features_train = np.load(
'../models/bottleneck_features_train_{}_{}.npy'.format(ts, name))
features_valid = np.load(
'../models/bottleneck_features_validation_{}_{}.npy'.format(
ts, name))
features_test = np.load(
'../models/bottleneck_features_test_{}_{}.npy'.format(ts, name))
# Rescale these features!
def min_max_scaling(features, min, max):
return ((features - min) / (max - min))
train_max = np.max(features_train)
train_min = np.min(features_train)
features_train = min_max_scaling(features_train, train_min, train_max)
features_valid = min_max_scaling(features_valid, train_min, train_max)
features_test = min_max_scaling(features_test, train_min, train_max)
# --- Pretrain the top model --- #
print('Pretraining top model...')
model = make_top_model(features_train.shape, field_size, nodes)
callbacks = [
EarlyStopping(monitor='val_loss', patience=4, verbose=1),
ModelCheckpoint('../models/GFM_top_{}_{}.h5'.format(logger.ts, name),
monitor='val_loss',
save_best_only=True,
verbose=1)
]
train_labels = [
np.array(
[output_fields_train[j][i] for j in range(len(features_train))])
for i in range(17)
]
valid_labels = [
np.array([
output_fields_validation[j][i] for j in range(len(features_valid))
]) for i in range(17)
]
history = model.fit(features_train,
train_labels,
callbacks=callbacks,
validation_data=(features_valid, valid_labels),
epochs=epochs,
batch_size=batch_size,
verbose=1)
# Store best model
model.load_weights('../models/GFM_top_{}_{}.h5'.format(logger.ts, name))
model.compile(loss='binary_crossentropy', optimizer='Adam')
top_model_path = '../models/top_model_{}_{}.h5'.format(ts, name)
model.save(top_model_path)
print('Done.')
# --- Reconstruct VGG model and finetune top conv layer --- #
print('Finetuning VGG...')
model, optimizer = reconstruct_VGG(
'../models/top_model_{}_{}.h5'.format(logger.ts, name), size,
features_train.shape, field_size, nodes, logger.ts, name, finetune,
optimizer)
if load_weights:
print('Loading pretrained weights...')
# load weights from a previous model run
assert size == 128, "weights only available for size 128"
model.load_weights(
'../models/GFM_VGG/VGG_GFM10072017_17:16_GFM_pre_128.h5')
# Finetune the model
callbacks = [
EarlyStopping(monitor='val_loss', patience=4, verbose=1),
ModelCheckpoint('../models/VGG_GFM{}_{}.h5'.format(logger.ts, name),
monitor='val_loss',
save_best_only=True,
verbose=1),
ReduceLROnPlateau(monitor='val_loss',
factor=0.1,
patience=2,
cooldown=2,
verbose=1)
]
model.fit_generator(generator=training_generator,
steps_per_epoch=n_train_files / batch_size,
epochs=epochs,
callbacks=callbacks,
validation_data=(validation_generator),
validation_steps=n_validation_files / batch_size)
print('Done.')
# Load best model
model.load_weights('../models/VGG_GFM{}_{}.h5'.format(logger.ts, name))
model.compile(loss='binary_crossentropy',
optimizer=optimizer,
metrics=['accuracy'])
# Make predictions for training, for validation and for data. With TTA!
# Call generators inside the loop!
print('TTA ({} loops)...'.format(TTA))
predictions_train = []
predictions_valid = []
predictions_test = []
for i in range(TTA):
training_generator_TTA = gen_augmentation.flow_from_directory(
train_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
validation_generator_TTA = gen_augmentation.flow_from_directory(
validation_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
test_generator_TTA = gen_augmentation.flow_from_directory(
test_directory,
target_size=(size, size),
class_mode=None,
batch_size=batch_size,
shuffle=False)
predictions_train.append(
model.predict_generator(generator=training_generator_TTA,
steps=n_train_files / batch_size,
verbose=1))
predictions_valid.append(
model.predict_generator(generator=validation_generator_TTA,
steps=n_validation_files / batch_size,
verbose=1))
predictions_test.append(
model.predict_generator(generator=test_generator_TTA,
steps=n_test_files / batch_size,
verbose=1))
print('Done.')
# Average TTA predictions
def average_TTA(predictions, TTA):
"""Average TTA predictions for GFM output
Input
----
predictions: list of len TTA
"""
return ([
np.mean([np.array(predictions[i][j]) for i in range(TTA)], axis=0)
for j in range(17)
])
predictions_train_avg = average_TTA(predictions_train, TTA)
predictions_valid_avg = average_TTA(predictions_valid, TTA)
predictions_test_avg = average_TTA(predictions_test, TTA)
# Fill up the predictions so that they have length 17
predictions_train_filled = []
predictions_valid_filled = []
predictions_test_filled = []
for pred in predictions_train_avg:
predictions_train_filled.append(GFM.complete_pred(pred[:, 1:], 17))
for pred in predictions_valid_avg:
predictions_valid_filled.append(GFM.complete_pred(pred[:, 1:], 17))
for pred in predictions_test_avg:
predictions_test_filled.append(GFM.complete_pred(pred[:, 1:], 17))
W = GFM.matrix_W_F2(beta=2, n_labels=17)
(optimal_predictions_train, E_F_train) = GFM.GFM(17, n_train_files,
predictions_train_filled,
W)
(optimal_predictions_valid, E_F_valid) = GFM.GFM(17, n_validation_files,
predictions_valid_filled,
W)
(optimal_predictions_test, E_F_test) = GFM.GFM(17, n_test_files,
predictions_test_filled, W)
score_GFM_train = fbeta_score(y_train,
optimal_predictions_train,
beta=2,
average='samples')
print(
'F_2 score on the training data with GFM: {}'.format(score_GFM_train))
score_GFM_valid = fbeta_score(y_valid,
optimal_predictions_valid,
beta=2,
average='samples')
print('F_2 score on the validation data with GFM: {}'.format(
score_GFM_valid))
# -------Store-------- #
if float(score_GFM_valid) > treshold:
# Save test predictions for submission
# Convert binary predictions to label strings - define a mapping to the file names
preds = [
' '.join(np.array(labels)[pred_row == 1])
for pred_row in optimal_predictions_test
]
test_files = [
f.split('.')[0]
for f in os.listdir('../data/interim/consensus_test/test/')
]
test_mapping = dict(zip([f for f in test_files], preds))
# Map the predictions to filenames in df_test
predictions_df = pd.DataFrame({
'image_name': df_test.image_name,
'tags': df_test.image_name
})
predictions_df['tags'] = predictions_df['tags'].map(test_mapping)
predictions_df.to_csv(
'../logs/predictions/GFM_VGG_{}_{}_{}.csv'.format(
ts, name, score_GFM_valid),
index=False)
# Save training set predictions to optimize ensembling algorithms
preds = [
' '.join(np.array(labels)[pred_row == 1])
for pred_row in optimal_predictions_train
]
train_mapping = dict(zip([f for f in df_train.image_name], preds))
predictions_df = pd.DataFrame({
'image_name': df_train.image_name,
'tags': df_train.image_name
})
predictions_df['tags'] = predictions_df['tags'].map(train_mapping)
predictions_df.to_csv(
'../logs/training_predictions/GFM_VGG_{}_{}_{}.csv'.format(
ts, name, score_GFM_valid),
index=False)
# Save validation set predictions
preds = [
' '.join(np.array(labels)[pred_row == 1])
for pred_row in optimal_predictions_valid
]
valid_mapping = dict(zip([f for f in df_train.image_name], preds))
predictions_df = pd.DataFrame({
'image_name': df_train.image_name,
'tags': df_train.image_name
})
predictions_df['tags'] = predictions_df['tags'].map(valid_mapping)
predictions_df.to_csv(
'../logs/training_predictions/GFM_VGG_validation_{}_{}_{}.csv'.
format(ts, name, score_GFM_valid),
index=False)
else:
logger.log_event('Low score - not storing anything.')
# Remove temp folders
du.remove_temp_dirs(logger.ts, name)
elapsed_time = time.time() - start_time
print('Elapsed time: {} minutes'.format(np.round(elapsed_time / 60, 2)))
print('Done.')
# Store the predictions for the matrix P and the F-optimal predictions to analyze them
# Also store y_train and the labels
import pickle
# train
with open('../logs/pickles/{}_{}_P_train'.format(ts, name), 'wb') as fp:
pickle.dump(predictions_train_filled, fp)
with open('../logs/pickles/{}_{}_p_train'.format(ts, name), 'wb') as fp:
pickle.dump(optimal_predictions_train, fp)
with open('../logs/pickles/{}_{}_y_train'.format(ts, name), 'wb') as fp:
pickle.dump(y_train, fp)
with open('../logs/pickles/{}_{}_filenames'.format(ts, name), 'wb') as fp:
pickle.dump(training_generator_TTA.filenames, fp)
# test
with open('../logs/pickles/{}_{}_P_test'.format(ts, name), 'wb') as fp:
pickle.dump(predictions_test_filled, fp)
with open('../logs/pickles/{}_{}_p_test'.format(ts, name), 'wb') as fp:
pickle.dump(optimal_predictions_test, fp)
with open('../logs/pickles/{}_{}_filenames_test'.format(ts, name),
'wb') as fp:
pickle.dump(test_generator_TTA.filenames, fp)
elapsed_time = time.time() - start_time
print('Elapsed time: {} minutes'.format(np.round(elapsed_time / 60, 2)))