def main(args):
# Used for memory error in RTX2070
physical_devices = tf.config.experimental.list_physical_devices('GPU')
config = tf.config.experimental.set_memory_growth(physical_devices[0],
True)
input_size = (None, None)
# Load model from JSON file if file path was provided...
if os.path.exists(args.model):
try:
with open(args.model, 'r') as f:
json = f.read()
model = model_from_json(json)
args.model = os.path.splitext(os.path.split(args.model)[-1])[0]
except JSONDecodeError:
raise ValueError(
"JSON decode error found. File path %s exists but could not be decoded; verify if JSON encoding was "
"performed properly." % args.model)
# ...Otherwise, create model from this project by using a proper key name
else:
model = models_dict[args.model]((input_size[0], input_size[1], 1))
try:
# Model name should match with the name of a model from
# https://www.tensorflow.org/api_docs/python/tf/keras/applications/
# This assumes you used a model with RGB inputs as the first part of your model,
# therefore your input data should be preprocessed with the corresponding
# 'preprocess_input' function
m = importlib.import_module('tensorflow.keras.applications.%s' %
model.name)
rgb_preprocessor = getattr(m, "preprocess_input")
except ModuleNotFoundError:
rgb_preprocessor = None
# Load trained weights
model.load_weights(args.pretrained_weights)
# Model is compiled to provide the desired metrics
model.compile(optimizer=Adam(lr=1e-4),
loss=custom_losses.bce_dsc_loss(3.0),
metrics=[
custom_losses.dice_coef,
keras_metrics.Precision(),
keras_metrics.Recall()
])
# Here we find to paths to all images from the selected datasets
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
for path in paths[0, :]:
[im, gt, pred] = data.test_image_from_path(model, path, None,
rgb_preprocessor)
name = os.path.split(path)[-1]
name, extension = os.path.splitext(name)
extension = ".png"
if not os.path.exists(args.save_to) and path != '':
os.makedirs(args.save_to)
cv2.imwrite(os.path.join(args.save_to, name + extension),
255 * np.where(pred > 0.5, 1.0, 0.0))
def main(args):
input_size = (None, None)
# Load model from JSON file if file path was provided...
if os.path.exists(args.model):
try:
with open(args.model, 'r') as f:
json = f.read()
model = model_from_json(json)
args.model = os.path.splitext(os.path.split(args.model)[-1])[0]
except JSONDecodeError:
raise ValueError(
"JSON decode error found. File path %s exists but could not be decoded; verify if JSON encoding was "
"performed properly." % args.model)
# ...Otherwise, create model from this project by using a proper key name
else:
model = models_dict[args.model]((input_size[0], input_size[1], 1))
try:
# Model name should match with the name of a model from
# https://www.tensorflow.org/api_docs/python/tf/keras/applications/
# This assumes you used a model with RGB inputs as the first part of your model,
# therefore your input data should be preprocessed with the corresponding
# 'preprocess_input' function
m = importlib.import_module('tensorflow.keras.applications.%s' % model.name)
rgb_preprocessor = getattr(m, "preprocess_input")
except ModuleNotFoundError:
rgb_preprocessor = None
# Load trained weights
model.load_weights(args.pretrained_weights)
# Model is compiled to provide the desired metrics
model.compile(optimizer=Adam(lr=1e-4), loss=custom_losses.bce_dsc_loss(3.0),
metrics=[custom_losses.dice_coef, keras_metrics.Precision(), keras_metrics.Recall()])
# Here we find to paths to all images from the selected datasets
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
print("Evaluating the model...")
data.save_results_on_paths(model, paths, args.save_to)
metrics = model.evaluate(x=data.validation_image_generator(paths, batch_size=1, rgb_preprocessor=rgb_preprocessor),
steps=paths.shape[1])
result_string = "Dataset: %s\nModel: %s\n" % ("/".join(args.dataset_names), args.model)
for idx, metric in enumerate(model.metrics_names):
result_string += "{}: {:.4f}\n".format(metric, metrics[idx])
for attribute in args.__dict__.keys():
result_string += "\n--%s: %s" % (attribute, str(args.__getattribute__(attribute)))
with open(os.path.join(args.save_to, "results.txt"), "w") as f:
f.write(result_string.strip())
def main(args):
start = datetime.now().strftime("%d-%m-%Y_%H.%M")
results_dir = "results_%s" % start
results_train_dir = os.path.join(results_dir, "results_training")
results_train_min_loss_dir = results_train_dir + "_min_val_loss"
results_validation_dir = os.path.join(results_dir, "results_validation")
results_validation_min_loss_dir = results_validation_dir + "_min_val_loss"
input_size = (None, None)
# Load model from JSON file if file path was provided...
if os.path.exists(args.model):
try:
with open(args.model, 'r') as f:
json = f.read()
model = model_from_json(json)
args.model = os.path.splitext(os.path.split(args.model)[-1])[0]
except JSONDecodeError:
raise ValueError(
"JSON decode error found. File path %s exists but could not be decoded; verify if JSON encoding was "
"performed properly." % args.model)
# ...Otherwise, create model from this project by using a proper key name
else:
model = models_dict[args.model]((input_size[0], input_size[1], 1))
try:
# Model name should match with the name of a model from
# https://www.tensorflow.org/api_docs/python/tf/keras/applications/
# This assumes you used a model with RGB inputs as the first part of your model,
# therefore your input data should be preprocessed with the corresponding
# 'preprocess_input' function
m = importlib.import_module('tensorflow.keras.applications.%s' %
model.name)
rgb_preprocessor = getattr(m, "preprocess_input")
except ModuleNotFoundError:
rgb_preprocessor = None
# We don't resize images for training, but provide image patches of reduced size for memory saving
# An image is turned into this size patches in a chess-board-like approach
input_size = args.training_crop_size
# For fine tuning, one can provide previous weights
if args.pretrained_weights:
model.load_weights(args.pretrained_weights)
# Model is compiled so it can be trained
model.compile(optimizer=Adam(lr=args.learning_rate),
loss=custom_losses.bce_dsc_loss(args.alpha),
metrics=[
custom_losses.dice_coef, 'binary_crossentropy',
keras_metrics.Precision(),
keras_metrics.Recall()
])
# Here we find to paths to all images from the selected datasets
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
# Data is split into 80% for training data and 20% for validation data. A custom seed is used for reproducibility.
n_training_images = int(0.8 * paths.shape[1])
np.random.seed(0)
np.random.shuffle(paths.transpose())
training_paths = paths[:, :n_training_images]
validation_paths = paths[:, n_training_images:]
# If asked by the user, save the paths of the validation split (useful to validate later)
if args.save_validation_paths:
with open("validation_paths.txt", "w+") as file:
print("Validation paths saved to 'validation_paths.txt'")
file.write("\n".join(
[";".join(paths) for paths in validation_paths.transpose()]))
# As input images can be of different sizes, here we calculate the total number of patches used for training.
print(
"Calculating the total number of samples after cropping and data augmentatiton. "
"This may take a while, don't worry.")
n_train_samples = next(
data.train_image_generator(training_paths,
input_size,
args.batch_size,
count_samples_mode=True,
rgb_preprocessor=None,
data_augmentation=args.use_da))
print("\nProceeding to train.")
# A customized early stopping callback. At each epoch end, the callback will test the current weights on the
# validation set (using whole images instead of patches) and stop the training if the minimum validation loss hasn't
# improved over the last 'patience' epochs.
es = EarlyStoppingAtMinValLoss(validation_paths,
file_path='%s_best.hdf5' % args.model,
patience=args.patience,
rgb_preprocessor=rgb_preprocessor)
reduce_lr = ReduceLROnPlateau(monitor='val_loss', factor=0.5, patience=5)
tensorboard = tf.keras.callbacks.TensorBoard(log_dir="logs")
# Training begins. Note that the train image generator can use or not data augmentation through the parsed argument
# 'use_da'
print("Start!")
try:
history = model.fit(x=data.train_image_generator(
training_paths,
input_size,
args.batch_size,
rgb_preprocessor=rgb_preprocessor,
data_augmentation=args.use_da),
epochs=args.epochs,
verbose=1,
callbacks=[es, reduce_lr, tensorboard],
steps_per_epoch=n_train_samples // args.batch_size)
print("Finished!")
except KeyboardInterrupt:
# This assumes a user keyboard interruption, as a hard early stop
print("Training interrupted. Only the best model will be saved.")
# Load the weights from the epoch with the minimum validation loss
model.load_weights('%s_best.hdf5' % args.model)
args.epochs = 0
# Save the weights of the last training epoch. If trained on a single epoch, these weights are equal to the
# best weights (to avoid redundancy, no new weights file is saved)
if args.epochs > 0:
model.save_weights("%s.hdf5" % args.model)
print("Last epoch's weights saved.")
print("Evaluating the model...")
print("On training paths:")
data.save_results_on_paths(model, training_paths, results_train_dir)
if args.epochs > 0:
os.replace("%s.hdf5" % args.model,
os.path.join(results_train_dir, "%s.hdf5" % args.model))
else:
model.save_weights(
os.path.join(results_train_dir, "%s.hdf5" % args.model))
print("\nOn validation paths:")
data.save_results_on_paths(model, validation_paths, results_validation_dir)
# Evaluate the model quantitatively by using the tensorflow model's metrics
metrics = model.evaluate(x=data.validation_image_generator(
validation_paths, batch_size=1, rgb_preprocessor=rgb_preprocessor),
steps=validation_paths.shape[1])
result_string = "Dataset: %s\nModel: %s\n" % ("/".join(
args.dataset_names), args.model)
for idx, metric in enumerate(model.metrics_names):
result_string += "{}: {:.4f}\n".format(metric, metrics[idx])
for attribute in args.__dict__.keys():
result_string += "\n--%s: %s" % (attribute,
str(args.__getattribute__(attribute)))
with open(os.path.join(results_validation_dir, "results.txt"), "w") as f:
f.write(result_string.strip())
# If the model was trained more than one epoch, evaluate the best validation weights in the same validation data.
# Otherwise, the best validation weights are the weights at the end of the only training epoch
if args.epochs > 1:
# Load results using the min val loss epoch's weights
model.load_weights('%s_best.hdf5' % args.model)
print("Evaluating the model with minimum validation loss...")
print("On training paths:")
data.save_results_on_paths(model, training_paths,
results_train_min_loss_dir)
print("\nOn validation paths:")
data.save_results_on_paths(model, validation_paths,
results_validation_min_loss_dir)
os.replace(
'%s_best.hdf5' % args.model,
os.path.join(results_train_min_loss_dir,
'%s_best.hdf5' % args.model))
metrics = model.evaluate(x=data.validation_image_generator(
validation_paths, batch_size=1, rgb_preprocessor=rgb_preprocessor),
steps=validation_paths.shape[1])
result_string = "Dataset: %s\nModel: %s\n" % ("/".join(
args.dataset_names), args.model)
for idx, metric in enumerate(model.metrics_names):
result_string += "{}: {:.4f}\n".format(metric, metrics[idx])
for attribute in args.__dict__.keys():
result_string += "\n--%s: %s" % (
attribute, str(args.__getattribute__(attribute)))
with open(os.path.join(results_validation_min_loss_dir, "results.txt"),
"w") as f:
f.write(result_string.strip())
# If trained more than one epoch, save the training history as csv and plot it
print("\nPlotting training history...")
import pandas as pd
pd.DataFrame.from_dict(history.history).to_csv(os.path.join(
results_dir, "training_history.csv"),
index=False)
# summarize history for loss
for key in history.history.keys():
plt.plot(history.history[key])
plt.ylim((0.0, 1.0 + args.alpha))
plt.title('model losses')
plt.ylabel('value')
plt.xlabel('epoch')
plt.legend(history.history.keys(), loc='upper left')
plt.savefig(os.path.join(results_dir, "training_losses.png"))
def main(args):
input_size = (256, 256)
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
n_training_images = int(0.8 * paths.shape[1])
np.random.seed(0)
np.random.shuffle(paths.transpose())
training_paths = paths[:, :n_training_images]
test_paths = paths[:, n_training_images:]
n_train_samples = next(
data.train_image_generator(training_paths,
input_size,
1,
resize=False,
count_samples_mode=True,
rgb_preprocessor=None))
from itertools import chain, combinations
def powerset(iterable):
"powerset([1,2,3]) --> () (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3)"
s = list(iterable)
return chain.from_iterable(
combinations(s, r) for r in range(len(s) + 1))
space = {
'alpha':
hp.choice('alpha', [0.3, 3.0, 5.0]),
'learning_rate':
hp.choice('learning_rate', [0.001, 0.0005, 0.0001, 0.00005, 0.00001]),
'train_vgg':
hp.choice('train_vgg', [True, False])
}
metric_score = "dice_coef"
def f_nn(params):
vgg19 = VGG19(include_top=False,
weights='imagenet',
input_tensor=None,
input_shape=(None, None, 3),
pooling=None)
encoder = Model(vgg19.input,
vgg19.get_layer("block5_conv4").output,
name="encoder")
# encoder.trainable = params["train_vgg"]
for layer in encoder.layers:
if layer.name.startswith("block5_conv"):
layer.trainable = params["train_vgg"]
d_i = Input(shape=(encoder.output.shape[1:]), name='decoder_input')
block5_up = UpSampling2D(size=(2, 2), name="block5_up")(d_i)
block4_1_conv0 = Conv2D(filters=512,
kernel_size=3,
padding='same',
activation='relu',
name="block4_1_conv0")(block5_up)
block4_merge = Concatenate(axis=-1, name="block4_merge")(
[vgg19.get_layer("block4_conv4").output, block4_1_conv0])
block4_1_conv1 = Conv2D(filters=512,
kernel_size=3,
padding='same',
activation='relu',
name="block4_1_conv1")(block4_merge)
block4_1_conv2 = Conv2D(filters=512,
kernel_size=3,
padding='same',
activation='relu',
name="block4_1_conv2")(block4_1_conv1)
block4_1_conv3 = Conv2D(filters=512,
kernel_size=3,
padding='same',
activation='relu',
name="block4_1_conv3")(block4_1_conv2)
block4_1_conv4 = Conv2D(filters=512,
kernel_size=3,
padding='same',
activation='relu',
name="block4_1_conv4")(block4_1_conv3)
block4_up = UpSampling2D(size=(2, 2), name="block4_up")(block4_1_conv4)
block3_1_conv0 = Conv2D(filters=256,
kernel_size=3,
padding='same',
activation='relu',
name="block3_1_conv0")(block4_up)
block3_merge = Concatenate(axis=-1, name="block3_merge")(
[vgg19.get_layer("block3_conv4").output, block3_1_conv0])
block3_1_conv1 = Conv2D(filters=256,
kernel_size=3,
padding='same',
activation='relu',
name="block3_1_conv1")(block3_merge)
block3_1_conv2 = Conv2D(filters=256,
kernel_size=3,
padding='same',
activation='relu',
name="block3_1_conv2")(block3_1_conv1)
block3_1_conv3 = Conv2D(filters=256,
kernel_size=3,
padding='same',
activation='relu',
name="block3_1_conv3")(block3_1_conv2)
block3_1_conv4 = Conv2D(filters=256,
kernel_size=3,
padding='same',
activation='relu',
name="block3_1_conv4")(block3_1_conv3)
block3_up = UpSampling2D(size=(2, 2), name="block3_up")(block3_1_conv4)
block2_1_conv0 = Conv2D(filters=128,
kernel_size=3,
padding='same',
activation='relu',
name="block2_1_conv0")(block3_up)
block2_merge = Concatenate(axis=-1, name="block2_merge")(
[vgg19.get_layer("block2_conv2").output, block2_1_conv0])
block2_1_conv1 = Conv2D(filters=128,
kernel_size=3,
padding='same',
activation='relu',
name="block2_1_conv1")(block2_merge)
block2_1_conv2 = Conv2D(filters=128,
kernel_size=3,
padding='same',
activation='relu',
name="block2_1_conv2")(block2_1_conv1)
block2_up = UpSampling2D(size=(2, 2), name="block2_up")(block2_1_conv2)
block1_1_conv0 = Conv2D(filters=64,
kernel_size=3,
padding='same',
activation='relu',
name="block1_1_conv0")(block2_up)
block1_merge = Concatenate(axis=-1, name="block1_merge")(
[vgg19.get_layer("block1_conv2").output, block1_1_conv0])
block1_1_conv1 = Conv2D(filters=64,
kernel_size=3,
padding='same',
activation='relu',
name="block1_1_conv1")(block1_merge)
block1_1_conv2 = Conv2D(filters=64,
kernel_size=3,
padding='same',
activation='relu',
name="block1_1_conv2")(block1_1_conv1)
block1_1_conv3 = Conv2D(filters=2,
kernel_size=3,
padding='same',
activation='relu',
name="block1_1_conv3")(block1_1_conv2)
output = Conv2D(filters=1,
kernel_size=1,
activation='sigmoid',
name="output")(block1_1_conv3)
decoder = Model([vgg19.input, d_i], output, name="decoder")
decoder_output = decoder([vgg19.input, encoder(encoder.input)])
model = Model(encoder.input, decoder_output, name=vgg19.name)
try:
# Model name should match with the name of a model from
# https://www.tensorflow.org/api_docs/python/tf/keras/applications/
# This assumes you used a model with RGB inputs as the first part of your model,
# therefore your input data should be preprocessed with the corresponding
# 'preprocess_input' function
m = importlib.import_module('tensorflow.keras.applications.%s' %
model.name)
rgb_preprocessor = getattr(m, "preprocess_input")
except ModuleNotFoundError:
rgb_preprocessor = None
my_loss = custom_losses.bce_dsc_loss(params["alpha"])
metrics_list = [
custom_losses.dice_coef,
keras_metrics.Precision(),
keras_metrics.Recall()
]
model.compile(optimizer=Adam(lr=params["learning_rate"]),
loss=my_loss,
metrics=metrics_list,
experimental_run_tf_function=False)
es = EarlyStoppingAtMinValLoss(test_paths,
file_path="best_test_weights.hdf5",
patience=20,
rgb_preprocessor=rgb_preprocessor)
history = model.fit(x=data.train_image_generator(
training_paths,
input_size,
args.batch_size,
resize=False,
rgb_preprocessor=rgb_preprocessor),
epochs=args.epochs,
verbose=0,
callbacks=[es],
steps_per_epoch=n_train_samples // 4)
metrics = model.evaluate(x=data.test_image_generator(
test_paths,
input_size=None,
batch_size=1,
rgb_preprocessor=rgb_preprocessor),
steps=test_paths.shape[1],
verbose=0)
for idx, metric in enumerate(model.metrics_names):
if metric == metric_score:
loss = metrics[idx]
break
try:
with open("best_%s.txt" % metric_score, "r") as f:
best_metric_score = float(f.read())
except FileNotFoundError:
best_metric_score = 0
if loss > best_metric_score:
with open("best_%s.txt" % metric_score, "w") as f:
f.write(str(loss))
model_json = model.to_json()
with open("best_metric_score_model.json", "w") as json_file:
json_file.write(model_json)
model.load_weights("best_test_weights.hdf5")
model.save_weights("best_%s_weights.hdf5" % metric_score)
data.save_results_on_paths(model,
training_paths,
"results_training",
rgb_preprocessor=rgb_preprocessor)
data.save_results_on_paths(model,
test_paths,
"results_test",
rgb_preprocessor=rgb_preprocessor)
os.remove("best_test_weights.hdf5")
with open("hyperparameter_search_result.txt", "a+") as f:
f.write("{} {:.4f}, {}\n".format(metric_score, loss, params))
plt.clf()
for key in history.history.keys():
if key in ["val_%s" % metric_score, metric_score]:
plt.plot(history.history[key])
plt.ylim((0.0, 1.0))
plt.title('model losses')
plt.ylabel('value')
plt.xlabel('epoch')
plt.legend([
key for key in history.history.keys()
if key in ["val_%s" % metric_score, metric_score]
],
loc='upper left')
global iteration
iteration += 1
if not os.path.exists("training_histories"):
os.makedirs("training_histories")
plt.savefig(
os.path.join("training_histories",
"history_iteration_%s.png" % iteration))
tf.keras.backend.clear_session()
print('Test %s:' % metric_score, loss)
print('Params: %s' % str(params))
return {'loss': -loss, 'status': STATUS_OK}
try: # try to load an already saved trials object, and increase the max
trials = pickle.load(open("my_model.hyperopt", "rb"))
print("Found saved Trials! Loading...")
print("Rerunning from {} trials to {} (+{}) trials".format(
len(trials.trials), len(trials.trials), args.fmin_max_evals))
global iteration
iteration += len(trials.trials)
args.fmin_max_evals = len(trials.trials) + args.fmin_max_evals
except: # create a new trials object and start searching
trials = Trials()
best = fmin(f_nn,
space,
algo=tpe.suggest,
max_evals=args.fmin_max_evals,
trials=trials)
print('best: ')
print(space_eval(space, best))
# save the trials object
with open("my_model.hyperopt", "wb") as f:
pickle.dump(trials, f)
result = "Best {}: {:.4f}\nParameters: {}\n\nDSC, Parameters\n".format(
metric_score, -trials.best_trial["result"]["loss"],
space_eval(space, best))
for trial in range(len(trials)):
trial_result = trials.results[trial]['loss']
trial_dict = {}
for key in trials.vals.keys():
trial_dict[key] = trials.vals[key][trial]
result += "{:.4f}, {}\n".format(-trial_result,
space_eval(space, trial_dict))
with open("hyperparameter_search_result.txt", "w") as f:
f.write(result.strip())
if os.path.exists("best_%s.txt" % metric_score):
os.remove("best_%s.txt" % metric_score)
def main(args):
# Used for memory error in RTX2070
physical_devices = tf.config.experimental.list_physical_devices('GPU')
config = tf.config.experimental.set_memory_growth(physical_devices[0],
True)
input_size = (None, None)
# Load model from JSON file if file path was provided...
if os.path.exists(args.model):
try:
with open(args.model, 'r') as f:
json = f.read()
model = model_from_json(json)
args.model = os.path.splitext(os.path.split(args.model)[-1])[0]
except JSONDecodeError:
raise ValueError(
"JSON decode error found. File path %s exists but could not be decoded; verify if JSON encoding was "
"performed properly." % args.model)
# ...Otherwise, create model from this project by using a proper key name
else:
model = models_dict[args.model]((input_size[0], input_size[1], 1))
try:
# Model name should match with the name of a model from
# https://www.tensorflow.org/api_docs/python/tf/keras/applications/
# This assumes you used a model with RGB inputs as the first part of your model,
# therefore your input data should be preprocessed with the corresponding
# 'preprocess_input' function
m = importlib.import_module('tensorflow.keras.applications.%s' %
model.name)
rgb_preprocessor = getattr(m, "preprocess_input")
except ModuleNotFoundError:
rgb_preprocessor = None
# Load trained weights
model.load_weights(args.pretrained_weights)
# Model is compiled to provide the desired metrics
model.compile(optimizer=Adam(lr=1e-4),
loss=custom_losses.bce_dsc_loss(3.0),
metrics=[
custom_losses.dice_coef,
keras_metrics.Precision(),
keras_metrics.Recall()
])
# Here we find to paths to all images from the selected datasets
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
header = np.array([["Image", "GT avg", "GT std", "Pred avg", "Pred std"]])
statistics = []
for im_path, gt_path in paths.transpose():
[im, gt, pred] = data.test_image_from_path(model, im_path, gt_path,
rgb_preprocessor)
gt_masked = im[np.where(gt >= 0.5)]
pred_masked = im[np.where(pred[..., 0] >= 0.5)]
gt_mean = round(np.mean(gt_masked), 4)
gt_std = round(np.std(gt_masked), 4)
pred_mean = round(np.mean(pred_masked), 4)
pred_std = round(np.std(pred_masked), 4)
statistics.append([
im_path,
str(gt_mean),
str(gt_std),
str(pred_mean),
str(pred_std)
])
statistics = np.array(statistics)
footer = np.array([[
"Average",
str(round(np.mean(statistics[:, 1].astype(np.float)), 4)),
str(round(np.mean(statistics[:, 2].astype(np.float)), 4)),
str(round(np.mean(statistics[:, 3].astype(np.float)), 4)),
str(round(np.mean(statistics[:, 4].astype(np.float)), 4))
]])
result_folder, file_name = os.path.split(args.save_to)
if not os.path.exists(result_folder) and result_folder != "":
os.makedirs(result_folder)
pandas.DataFrame(np.concatenate((header, statistics, footer),
axis=0)).to_csv(args.save_to,
header=None,
index=None)
def main(args):
if args.resize_inputs_to == [-1, -1]:
args.resize_inputs_to = [None, None]
input_size = tuple(args.resize_inputs_to)
model, loss = models_dict[args.model]((input_size[0], input_size[1], 1),
latent_dim=args.latent_space_dim,
self_supervised=args.self_supervised)
def rescale(image):
return image / 255.0
rgb_preprocessor = rescale
if input_size == (None, None):
input_size = (256, 256)
if args.pretrained_weights:
model.load_weights(args.pretrained_weights)
metrics_list = ['mse'] if args.self_supervised else \
[custom_losses.dice_coef, keras_metrics.Precision(), keras_metrics.Recall()]
model.compile(optimizer=Adam(lr=args.learning_rate), loss=loss, metrics=metrics_list,
experimental_run_tf_function=False
)
paths = data.create_image_paths(args.dataset_names, args.dataset_paths)
# if args.self_supervised:
# paths[1, :] = paths[0, :]
n_training_images = int(0.8 * paths.shape[1])
np.random.seed(0)
np.random.shuffle(paths.transpose())
training_paths = paths[:, :n_training_images]
test_paths = paths[:, n_training_images:]
# n_train_samples = next(data.train_image_generator(training_paths, input_size, args.batch_size,
# resize=(model.input.shape.as_list()[1:-1] != [None, None]),
# normalize_x=args.normalize_input,
# rgb_preprocessor=rgb_preprocessor,
# count_samples_mode=True, data_augmentation=args.use_da))
# es = EarlyStoppingAtMinValLoss(test_paths, file_path='%s_best.hdf5' % args.model, patience=20,
# rgb_preprocessor=rgb_preprocessor)
#
# history = model.fit(x=data.train_image_generator(training_paths, input_size, args.batch_size,
# resize=(model.input.shape.as_list()[1:-1] != [None, None]),
# normalize_x=args.normalize_input,
# rgb_preprocessor=rgb_preprocessor,
# data_augmentation=args.use_da),
# epochs=args.epochs,
# verbose=1,
# callbacks=[es],
# steps_per_epoch=n_train_samples // args.batch_size)
n_train_samples = next(data.train_image_generator_clean(training_paths, input_size, args.batch_size,
resize=False,
normalize_x=args.normalize_input,
rgb_preprocessor=rgb_preprocessor,
count_samples_mode=True, data_augmentation=args.use_da))
es = EarlyStoppingAtMinValLoss_Clean(test_paths, file_path='%s_best.hdf5' % args.model, patience=20,
rgb_preprocessor=rgb_preprocessor, resize_nocrop=False, size=input_size,
normalize_input=args.normalize_input)
history = model.fit(x=data.train_image_generator_clean(training_paths, input_size, args.batch_size,
resize=False,
normalize_x=args.normalize_input,
rgb_preprocessor=rgb_preprocessor,
data_augmentation=args.use_da),
epochs=args.epochs,
verbose=1,
callbacks=[es],
steps_per_epoch=n_train_samples // args.batch_size)
if args.epochs > 0:
model.save_weights("%s.hdf5" % args.model)
evaluation_input_shape = tuple(model.input.shape[1:-1])
if evaluation_input_shape == (None, None):
evaluation_input_shape = None
# Save results using the last epoch's weights
data.save_results_on_paths(model, training_paths, "results_training", rgb_preprocessor=rgb_preprocessor)
data.save_results_on_paths(model, test_paths, "results_test", rgb_preprocessor=rgb_preprocessor)
# metrics = model.evaluate(x=data.test_image_generator(test_paths, evaluation_input_shape, batch_size=1,
# rgb_preprocessor=rgb_preprocessor,
# normalize_x=args.normalize_input),
# steps=test_paths.shape[1])
metrics = model.evaluate(x=data.train_image_generator_clean(training_paths, input_size, batch_size=1,
resize=False,
normalize_x=args.normalize_input,
rgb_preprocessor=rgb_preprocessor,
data_augmentation=False),
steps=test_paths.shape[1])
result_string = "Dataset: %s\nModel: %s\n" % ("/".join(args.dataset_names), args.model)
for idx, metric in enumerate(model.metrics_names):
result_string += "{}: {:.4f}\n".format(metric, metrics[idx])
for attribute in args.__dict__.keys():
result_string += "\n--%s: %s" % (attribute, str(args.__getattribute__(attribute)))
with open(os.path.join("results_test", "results.txt"), "w") as f:
f.write(result_string.strip())
if args.epochs > 1:
# Save results using the min val loss epoch's weights
model.load_weights('%s_best.hdf5' % args.model)
data.save_results_on_paths(model, training_paths, "results_training_min_val_loss", rgb_preprocessor=rgb_preprocessor)
data.save_results_on_paths(model, test_paths, "results_test_min_val_loss", rgb_preprocessor=rgb_preprocessor)
# metrics = model.evaluate(x=data.test_image_generator(test_paths, evaluation_input_shape, batch_size=1,
# rgb_preprocessor=rgb_preprocessor,
# normalize_x=args.normalize_input),
# steps=test_paths.shape[1])
metrics = model.evaluate(x=data.train_image_generator_clean(training_paths, input_size, batch_size=1,
resize=False,
normalize_x=args.normalize_input,
rgb_preprocessor=rgb_preprocessor,
data_augmentation=False),
steps=test_paths.shape[1])
result_string = "Dataset: %s\nModel: %s\n" % ("/".join(args.dataset_names), args.model)
for idx, metric in enumerate(model.metrics_names):
result_string += "{}: {:.4f}\n".format(metric, metrics[idx])
for attribute in args.__dict__.keys():
result_string += "\n--%s: %s" % (attribute, str(args.__getattribute__(attribute)))
with open(os.path.join("results_test_min_val_loss", "results.txt"), "w") as f:
f.write(result_string.strip())
# summarize history for loss
for key in history.history.keys():
plt.plot(history.history[key])
# plt.ylim((0.0, 1.0 + args.alpha))
plt.title('model losses')
plt.ylabel('value')
plt.xlabel('epoch')
plt.legend(history.history.keys(), loc='upper left')
plt.savefig("training_losses.png")