def main(cnf, weights_from):
config = util.load_module(cnf).config
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
labels = data.get_labels(names).astype(np.float32)
net = create_net(config)
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
print("Shape of files: " + str(files.shape))
print("Shape of labels: " + str(labels.shape))
start = time.time()
print("fitting ...")
net.fit(files, labels)
end = time.time()
print("Time elapsed for fitting: " + str(end - start))
def main(cnf, weights_from):
config = util.load_module(cnf).config
# print(config)
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
print(config.get('train_dir'))
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
labels = data.get_labels(names).astype(np.float32)
print("Checkpoint 5")
net = create_net(config)
print("Checkpoint 6")
print(weights_from)
# print(net.load_params_from())
try:
print("Checkpoint 7")
net.load_params_from(weights_from)
print("Checkpoint 8")
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
print("fitting ...")
print(files)
print(labels)
net.fit(files, labels)
def transform(cnf, n_iter, skip, test, train, weights_from, test_dir):
config = util.load_module(cnf).config
runs = {}
if train:
runs["train"] = config.get("train_dir")
if test or test_dir:
runs["test"] = test_dir or config.get("test_dir")
net = nn.create_net(config)
if weights_from is None:
net.load_params_from(config.weights_file)
print("loaded weights from {}".format(config.weights_file))
else:
weights_from = str(weights_from)
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
if n_iter > 1:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=config.cnf["sigma"], **config.cnf["aug_params"]
)
else:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=0.0, **data.no_augmentation_params
)
for run, directory in sorted(runs.items(), reverse=True):
print("extracting features for files in {}".format(directory))
tic = time.time()
files = data.get_image_files(directory)
Xs, Xs2 = None, None
for i, (tf, color_vec) in enumerate(zip(tfs, color_vecs), start=1):
print("{} transform iter {}".format(run, i))
X = net.transform(files, transform=tf, color_vec=color_vec)
if Xs is None:
Xs = X
Xs2 = X ** 2
else:
Xs += X
Xs2 += X ** 2
print("took {:6.1f} seconds".format(time.time() - tic))
if i % 5 == 0 or n_iter < 5:
std = np.sqrt((Xs2 - Xs ** 2 / i) / (i - 1))
config.save_features(Xs / i, i, skip=skip, test=True if run == "test" else False)
config.save_std(std, i, skip=skip, test=True if run == "test" else False)
print("saved {} iterations".format(i))
def transform(cnf=cnf,
n_iter=n_iter,
skip=skip,
test=test,
train=train,
weights_from=weights_from,
test_dir=test_dir):
config = util.load_module(cnf).config
config.cnf['batch_size_train'] = 128
config.cnf['batch_size_test'] = 128
runs = {}
if train:
runs['train'] = config.get('train_dir')
if test or test_dir:
runs['test'] = test_dir or config.get('test_dir')
net = nn.create_net(config)
if weights_from is None:
net.load_params_from(config.weights_file)
print("loaded weights from {}".format(config.weights_file))
else:
weights_from = str(weights_from)
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
if n_iter > 1:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter,
skip=skip,
color_sigma=config.cnf['sigma'],
**config.cnf['aug_params'])
else:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=0.0, **data.no_augmentation_params)
ret_val = []
for run, directory in sorted(runs.items(), reverse=True):
print("extracting features for files in {}".format(directory))
tic = time.time()
files = data.get_image_files(directory)
Xs, Xs2 = None, None
for i, (tf, color_vec) in enumerate(zip(tfs, color_vecs), start=1):
print("{} transform iter {}".format(run, i))
X = net.transform(files[:1000], transform=tf, color_vec=color_vec)
ret_val.append(X)
return ret_val, net
def main(cnf, classes, weights_from, predict):
config = util.load_module(cnf).config
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
names = [int(x) for x in names ]
data.classes = int(classes)
labels = data.get_labels(names)
net = create_net(config)
print files.shape
print labels.shape
if predict :
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
print weights_from
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
if not predict:
print("fitting ...")
net.fit(files, labels)
else:
print("predicting ...")
test_files = data.get_image_files(config.get('test_dir'))
y_pred = net.predict(test_files)
y_pred = y_pred.transpose()
print y_pred
y_pred = np.clip(np.round(y_pred),
np.min(labels), np.max(labels)).astype(int)
#print y_pred
submission_filename = util.get_submission_filename()
image_files = data.get_image_files(config.get('test_dir'))
names = data.get_names(image_files)
image_column = pd.Series(names, name='photo_id')
level_column = pd.DataFrame(y_pred)#name='labels')
level_column = level_column.apply(lambda x : string_submit(x))
predictions = pd.concat([image_column, level_column], axis=1)
print("tail of predictions file")
print(predictions.tail())
predictions.columns = ['photo_id', 'labels']
predictions.to_csv(submission_filename, index=False)
print("saved predictions to {}".format(submission_filename))
def main(cnf, classes, weights_from, predict):
config = util.load_module(cnf).config
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
names = [int(x) for x in names]
data.classes = int(classes)
labels = data.get_labels(names)
net = create_net(config)
print files.shape
print labels.shape
if predict:
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
print weights_from
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
if not predict:
print("fitting ...")
net.fit(files, labels)
else:
print("predicting ...")
test_files = data.get_image_files(config.get('test_dir'))
y_pred = net.predict(test_files)
y_pred = y_pred.transpose()
print y_pred
y_pred = np.clip(np.round(y_pred), np.min(labels),
np.max(labels)).astype(int)
#print y_pred
submission_filename = util.get_submission_filename()
image_files = data.get_image_files(config.get('test_dir'))
names = data.get_names(image_files)
image_column = pd.Series(names, name='photo_id')
level_column = pd.DataFrame(y_pred) #name='labels')
level_column = level_column.apply(lambda x: string_submit(x))
predictions = pd.concat([image_column, level_column], axis=1)
print("tail of predictions file")
print(predictions.tail())
predictions.columns = ['photo_id', 'labels']
predictions.to_csv(submission_filename, index=False)
print("saved predictions to {}".format(submission_filename))
def main(cnf, weights_from, fold, exp_run_folder, train_retina):
config = util.load_module(cnf).config
config.cnf[
'fold'] = fold # <-- used to change the directories for weights_best, weights_epoch and weights_final
config.cnf['exp_run_folder'] = exp_run_folder
protocol = data.settings['protocol']
if train_retina != 'train_retina':
folds = yaml.load(open('folds/' + protocol + '.yml'))
f0, f1 = fold.split('x')
train_list = folds['Fold_' + f0][int(f1) - 1]
files = data.get_image_files(config.get('train_dir'), train_list)
else:
files = data.get_image_files(config.get('train_dir'))
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
names = data.get_names(files)
labels = data.get_labels(names, label_file='folds/' + protocol +
'.csv').astype(np.int32)
net = nn.create_net(config)
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights, starting from scratch")
#Print layerinfo
print("## Layer information")
import nolearn
layer_info = nolearn.lasagne.PrintLayerInfo()
print(layer_info._get_greeting(net))
layer_info, legend = layer_info._get_layer_info_conv(net)
print(layer_info)
print(legend)
print("fitting ...")
net.fit(files, labels)
def main(cnf, weights_from):
config = util.load_module(cnf).config
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
labels = data.get_labels(names).astype(np.float32)
net = create_net(config)
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
print("fitting ...")
net.fit(files, labels)
def build(cnf, weights_from):
config = util.load_module(cnf).config
if weights_from is None:
weights_from = config.weights_file
else:
weights_from = str(weights_from)
files = data.get_image_files(config.get('train_dir'))
names = data.get_names(files)
labels = data.get_labels(names).astype(np.float32)
net = create_net(config)
try:
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
except IOError:
print("couldn't load weights starting from scratch")
print("fitting ...")
# net.fit(files, labels)
return net, files, names, labels
def transform(cnf, n_iter, skip, test, train, weights_from, test_dir):
config = util.load_module(cnf).config
config.cnf['batch_size_train'] = 128
config.cnf['batch_size_test'] = 128
runs = {}
if train:
runs['train'] = config.get('train_dir')
if test or test_dir:
runs['test'] = test_dir or config.get('test_dir')
net = nn.create_net(config)
if weights_from is None:
net.load_params_from(config.weights_file)
print("loaded weights from {}".format(config.weights_file))
else:
weights_from = str(weights_from)
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
if n_iter > 1:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter,
skip=skip,
color_sigma=config.cnf['sigma'],
**config.cnf['aug_params'])
else:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=0.0, **data.no_augmentation_params)
for run, directory in sorted(runs.items(), reverse=True):
print("extracting features for files in {}".format(directory))
tic = time.time()
files = data.get_image_files(directory)
Xs, Xs2 = None, None
for i, (tf, color_vec) in enumerate(zip(tfs, color_vecs), start=1):
print("{} transform iter {}".format(run, i))
X = net.transform(files, transform=tf, color_vec=color_vec)
if Xs is None:
Xs = X
Xs2 = X**2
else:
Xs += X
Xs2 += X**2
print('took {:6.1f} seconds'.format(time.time() - tic))
if i % 10 == 0 or n_iter < 5:
std = np.sqrt((Xs2 - Xs**2 / i) / (i - 1))
config.save_features(Xs / i,
i,
skip=skip,
test=True if run == 'test' else False)
config.save_std(std,
i,
skip=skip,
test=True if run == 'test' else False)
print('saved {} iterations'.format(i))
from __future__ import division
import time
import click
import numpy as np
import nn
import data_orig
import tta
import utils
cnf='configs/c_512_5x5_32.py'
config = utils.load_module(cnf).config
config.cnf['batch_size_train'] = 128
runs = {}
runs['train'] = config.get('train_dir')
net = nn.create_net(config)
weights_from = 'weights/c_512_5x5_32/weights_final.pkl'
net.load_params_from(weights_from)
tf, color_vecs = tta.build_quasirandom_transforms(1, skip=0, color_sigma=0.0, **data_orig.no_augmentation_params)
for i, (tf, color_vec) in enumerate(zip(tfs, color_vecs), start=1):
pass
def transform(cnf, exp_run_folder, n_iter, skip, test, train, weights_from, test_dir, fold):
config = util.load_module(cnf).config
config.cnf['fold'] = fold # <-- used to change the directories for weights_best, weights_epoch and weights_final
config.cnf['exp_run_folder'] = exp_run_folder
runs = {}
if train:
runs['train'] = config.get('train_dir')
if test or test_dir:
runs['test'] = test_dir or config.get('test_dir')
folds = yaml.load(open('folds/'+data.settings['protocol']+'.yml'))
f0, f1 = fold.split('x')
train_list = folds['Fold_' + f0][int(f1)-1]
test_list = folds['Fold_' + f0][0 if f1=='2' else 1]
net = nn.create_net(config)
if weights_from is None:
net.load_params_from(config.weights_file)
print("loaded weights from {}".format(config.weights_file))
else:
weights_from = str(weights_from)
net.load_params_from(weights_from)
print("loaded weights from {}".format(weights_from))
if n_iter > 1:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=config.cnf['sigma'],
**config.cnf['aug_params'])
else:
tfs, color_vecs = tta.build_quasirandom_transforms(
n_iter, skip=skip, color_sigma=0.0,
**data.no_augmentation_params)
for run, directory in sorted(runs.items(), reverse=True):
print("extracting features for files in {}".format(directory))
tic = time.time()
if run == 'train':
files = data.get_image_files(directory, train_list)
else:
files = data.get_image_files(directory, test_list)
Xs, Xs2 = None, None
for i, (tf, color_vec) in enumerate(zip(tfs, color_vecs), start=1):
print("{} transform iter {}".format(run, i))
X = net.transform(files, transform=tf, color_vec=color_vec)
if Xs is None:
Xs = X
Xs2 = X**2
else:
Xs += X
Xs2 += X**2
print('took {:6.1f} seconds'.format(time.time() - tic))
if i % 5 == 0 or n_iter < 5:
std = np.sqrt((Xs2 - Xs**2 / i) / (i - 1))
config.save_features_fold(Xs / i, i, skip=skip, fold=fold,
test=True if run == 'test' else False)
#config.save_std_fold(std, i, skip=skip, fold=fold,
# test=True if run == 'test' else False)
print('saved {} iterations'.format(i))
