def find_best_lr(batch_size=24, model_key=0):
base_path, morfeus_drive = return_paths()
excel_path = os.path.join(morfeus_drive, 'ModelParameters.xlsx')
min_lr = 1e-5
max_lr = 10
model_base = return_model(model_key=model_key)
loss = CosineLoss()
features_list = ('Model_Type', 'Optimizer', 'step_factor')
for iteration in [0, 1]:
for optimizer in ['SGD']:
out_path = os.path.join(morfeus_drive, 'Learning_Rates',
'Model_Key_{}'.format(model_key))
if not isinstance(model_base, types.FunctionType):
model = model_base
base_df = pd.read_excel(excel_path)
current_run = {
'Model_Type': [model_key],
'run?': [0],
'step_factor': [10],
'Loss': ['CosineLoss'],
'Optimizer': ['SGD']
}
current_run_df = pd.DataFrame(current_run)
contained = is_df_within_another(data_frame=base_df,
current_run_df=current_run_df,
features_list=('Model_Type',
'Optimizer',
'step_factor'))
if not contained:
model_index = 0
while model_index in base_df['Model_Index'].values:
model_index += 1
current_run_df.insert(0,
column='Model_Index',
value=model_index)
current_run_df.set_index('Model_Index')
base_df = base_df.append(current_run_df)
base_df.to_excel(excel_path, index=0)
else:
for key in features_list:
base_df = base_df.loc[base_df[key] ==
current_run_df[key].values[0]]
model_index = base_df.Model_Index.values[0]
out_path = os.path.join(out_path,
'Model_Index_{}'.format(model_index),
'{}_Iteration'.format(iteration))
if os.path.exists(out_path):
continue
else:
model, out_path = return_model_and_things(
model_base=model_base,
out_path=out_path,
iteration=iteration,
excel_path=excel_path)
if model is None:
continue
os.makedirs(out_path)
_, _, train_generator, validation_generator = return_generators(
batch_size=batch_size,
model_key=model_key,
cross_validation_id=-1,
cache=True)
print(out_path)
k = TensorBoard(log_dir=out_path,
profile_batch=0,
write_graph=True)
k.set_model(model)
k.on_train_begin()
if optimizer == 'SGD':
lr_opt = tf.keras.optimizers.SGD
elif optimizer == 'Adam':
lr_opt = tf.keras.optimizers.Adam
elif optimizer == 'RAdam':
lr_opt = RectifiedAdam
LearningRateFinder(epochs=10,
model=model,
metrics=['accuracy'],
out_path=out_path,
optimizer=lr_opt,
loss=loss,
steps_per_epoch=1000,
train_generator=train_generator.data_set,
lower_lr=min_lr,
high_lr=max_lr)
tf.keras.backend.clear_session()
return False # repeat!
return True
def train_model(epochs=None,
model_name='3D_Fully_Atrous',
run_best=False,
debug=False,
combined_lobes=False,
gaussian=False):
num_classes = 9
if combined_lobes:
num_classes = 6
save_a_model = False
if run_best:
save_a_model = True
batch_size = 1
step_size_factor = 8
for iteration in range(3):
base_path, morfeus_drive = return_paths()
base_dict = return_base_dict_dense(step_size_factor=step_size_factor)
overall_dictionary = return_dictionary_dense(base_dict,
run_best=run_best,
added_gaussian=gaussian)
overall_dictionary = np.asarray(overall_dictionary)
perm = np.arange(len(overall_dictionary))
np.random.shuffle(perm)
overall_dictionary = overall_dictionary[perm]
if debug:
i = 0
_, _, train_generator, validation_generator = return_generators()
for run_data in overall_dictionary:
run_data['num_classes'] = num_classes
run_data['pool_z'] = 4
run_data['save_a_model'] = save_a_model
if debug:
layers_dict = get_layers_dict_dense(**run_data, pool=(2, 4, 4))
model = my_UNet(layers_dict=layers_dict,
image_size=(None, None, None, 1),
mask_output=True,
concat_not_add=True,
out_classes=num_classes,
explictly_defined=True)
Model_val = model.created_model
Model_val.compile(tf.keras.optimizers.Adam(),
loss=tf.keras.losses.CategoricalCrossentropy(
from_logits=False),
metrics=[
tf.keras.metrics.CategoricalAccuracy(),
MeanDSC(num_classes=num_classes)
])
i += 1
k = TensorBoard(
log_dir=r'H:\Liver_Lobe_tensorboard\test\{}'.format(i),
profile_batch=0,
histogram_freq=5,
write_graph=True)
k.set_model(Model_val)
k.on_train_begin()
tf.keras.backend.clear_session()
continue
if debug:
return None
tf.random.set_seed(iteration)
run_data['batch_size'] = batch_size
excel_path = os.path.join(morfeus_drive,
'parameters_list_by_trial_id.xlsx')
print(base_path)
run_data['Iteration'] = iteration
run_data['Trial_ID'] = 0
features_list = list(run_data.keys())
if determine_if_in_excel(excel_path,
run_data,
features_list=features_list):
continue
trial_id = run_data['Trial_ID']
hparams = return_hparams(run_data,
features_list=features_list,
excluded_keys=[])
layers_dict = get_layers_dict_dense(**run_data, pool=(4, 4, 4))
paths_class = Path_Return_Class(base_path=base_path,
morfeus_path=morfeus_drive,
save_model=save_a_model,
is_keras_model=False)
paths_class.define_model_things(model_name,
'Trial_ID_{}'.format(trial_id))
tensorboard_output = paths_class.tensorboard_path_out
print(tensorboard_output)
if os.listdir(tensorboard_output):
print('already done')
continue
records_add = ''
if run_data['gaussian']:
records_add = '_Gaussian'
_, _, train_generator, validation_generator = return_generators(
combined_lobes=combined_lobes,
records_add=records_add,
change_background=run_data['change_background'])
step_size = len(train_generator)
run_model(trial_id=str(trial_id),
layers_dict=layers_dict,
train_generator=train_generator,
step_size=step_size,
validation_generator=validation_generator,
paths_class=paths_class,
morfeus_drive=morfeus_drive,
hparams=hparams,
base_path=base_path,
epochs=epochs,
**run_data)
return None # break out!
optimizer = AdamOptimizer(0.001)
tbcb = TensorBoard(log_dir='/logs',
histogram_freq=1,
write_graph=True,
write_grads=True,
write_images=True,
embeddings_freq=1)
loss_history = []
cos_loss_history = []
T = 0.0
t0 = time.time()
tbcb.set_model(model)
tbcb.on_train_begin()
f = open('log.txt', 'w')
try:
for epoch in range(200):
tbcb.on_epoch_begin(epoch)
cos_loss = CosineSimilarity()
for step in (range(num_batch)):
tbcb.on_train_batch_begin(step)
print('========== step: {:03d} / {:03d} ============\r'.format(
step, num_batch),
end='')
earlystop.on_train_begin()
modelcheckpoint = ModelCheckpoint(filepath="weights/",
monitor="val_loss",
verbose=1,
save_best_only=True)
modelcheckpoint.set_model(model)
modelcheckpoint.on_train_begin()
reduce_lr = ReduceLROnPlateau(monitor="val_loss", patience=10, verbose=1)
reduce_lr.set_model(model)
reduce_lr.on_train_begin()
tensorboard = TensorBoard(log_dir="logs/")
tensorboard.set_model(model)
tensorboard.on_train_begin()
epochs = 3
train_logs_dict = {}
test_logs_dict = {}
for epoch in range(epochs):
training_acc, testing_acc, training_loss, testing_loss = [], [], [], []
print("\nStart of epoch %d" % (epoch + 1, ))
# Iterate over the batches of the dataset.
modelcheckpoint.on_epoch_begin(epoch)
earlystop.on_epoch_begin(epoch)
reduce_lr.on_epoch_begin(epoch)
tensorboard.on_epoch_begin(epoch)
for x_batch_train, y_batch_train in get_batch(batch_size, x_train,
y_train):
def find_best_lr(path_desc='', combined_lobes=False, records_add=''):
min_lr = 1e-7
max_lr = 1e-1
num_classes = 9
if combined_lobes:
num_classes = 6
max_conv_blocks = 3
iteration = 0
change_background = True
for weighted_loss in [True, False]:
for atrous in [True, False]:
for layer in [2, 3]:
for growth_rate in [4]:
for filters in [8]:
for num_conv_blocks in [
2
]: # Always start with 1 before downsampling
for conv_lambda in [1]:
base_path, morfeus_drive = return_paths()
run_data = {
'layers': layer,
'max_conv_blocks': max_conv_blocks,
'filters': filters,
'num_conv_blocks': num_conv_blocks,
'conv_lambda': conv_lambda,
'growth_rate': growth_rate,
'atrous': atrous
}
layers_dict = get_layers_dict_dense(
**run_data,
pool=(2, 4, 4),
num_classes=num_classes)
things = [
'change_background{}'.format(
change_background),
'weighted_loss_{}'.format(weighted_loss),
'atrous_{}'.format(atrous),
'layers{}'.format(layer),
'max_conv_blocks_{}'.format(
max_conv_blocks),
'filters_{}'.format(filters),
'num_conv_blocks_{}'.format(
num_conv_blocks),
'conv_lambda_{}'.format(conv_lambda),
'growth_rate_{}'.format(growth_rate),
'{}_Iteration'.format(iteration)
]
out_path = os.path.join(
morfeus_drive, path_desc, 'DenseNet')
if records_add != '':
things = ['Gaussian'] + things
for thing in things:
out_path = os.path.join(out_path, thing)
if os.path.exists(out_path):
print('already done')
continue
os.makedirs(out_path)
print(out_path)
model = my_UNet(
layers_dict=layers_dict,
image_size=(None, None, None, 1),
mask_output=True,
out_classes=num_classes,
explictly_defined=True).created_model
k = TensorBoard(log_dir=out_path,
profile_batch=0,
write_graph=True)
k.set_model(model)
k.on_train_begin()
lr_opt = tf.keras.optimizers.Adam
base_path, morfeus_drive, train_generator, validation_generator = return_generators(
combined_lobes=combined_lobes,
records_add=records_add,
change_background=change_background)
loss = tf.keras.losses.CategoricalCrossentropy(
from_logits=False)
LearningRateFinder(
epochs=10,
model=model,
metrics=[
'categorical_accuracy',
MeanDSC(num_classes=num_classes)
],
out_path=out_path,
optimizer=lr_opt,
loss=loss,
steps_per_epoch=len(train_generator),
train_generator=train_generator.data_set,
lower_lr=min_lr,
high_lr=max_lr)
tf.keras.backend.clear_session()
return None # repeat!
def find_best_lr(batch_size=24):
tf.random.set_seed(3141)
base_path, morfeus_drive, excel_path = return_paths()
# if base_path.startswith('H'): # Only run this locally
# create_excel_values(excel_path=excel_path)
for iteration in [0]:
out_path = os.path.join(morfeus_drive, 'Learning_Rates')
model_parameters, out_path = return_model_parameters(
out_path=out_path, excel_path=excel_path, iteration=iteration)
if model_parameters is None:
continue
model_key = model_parameters['Model_Type']
optimizer = model_parameters['Optimizer']
model_base = return_model(model_key=model_key)
model = model_base(**model_parameters)
if model_parameters['loss'] == 'CosineLoss':
loss = CosineLoss()
min_lr = 1e-6
max_lr = 1e-1
elif model_parameters['loss'] == 'CategoricalCrossEntropy':
loss = tf.keras.losses.CategoricalCrossentropy()
min_lr = 1e-10
max_lr = 1e-3
_, _, train_generator, validation_generator = return_generators(
batch_size=batch_size,
model_key=model_key,
all_training=True,
cache=True,
cache_add='LR_Finder_{}'.format(model_key))
print(out_path)
k = TensorBoard(log_dir=out_path, profile_batch=0, write_graph=True)
k.set_model(model)
k.on_train_begin()
lr_opt = tf.keras.optimizers.Adam
if optimizer == 'SGD':
lr_opt = tf.keras.optimizers.SGD
elif optimizer == 'Adam':
lr_opt = tf.keras.optimizers.Adam
elif optimizer == 'RAdam':
lr_opt = RectifiedAdam
METRICS = [
metrics.TruePositives(name='TruePositive'),
metrics.FalsePositives(name='FalsePositive'),
metrics.TrueNegatives(name='TrueNegative'),
metrics.FalseNegatives(name='FalseNegative'),
metrics.CategoricalAccuracy(name='Accuracy'),
metrics.Precision(name='Precision'),
metrics.Recall(name='Recall'),
metrics.AUC(name='AUC'),
]
LearningRateFinder(epochs=10,
model=model,
metrics=METRICS,
out_path=out_path,
optimizer=lr_opt,
loss=loss,
steps_per_epoch=1000,
train_generator=train_generator.data_set,
lower_lr=min_lr,
high_lr=max_lr)
tf.keras.backend.clear_session()
return False # repeat!
return True
