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Merge remote-tracking branch 'pixelwise_local/ReduceLROnPlateau' into ReduceLROnPlateau
# Conflicts: # LICENSE # README.md # requirements.txt # train.py
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kba
commit
54132a499a
4 changed files with 174 additions and 37 deletions
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.gitkeep
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.gitkeep
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__init__.py
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__init__.py
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148
train.py
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train.py
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@ -31,6 +31,7 @@ os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
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import tensorflow as tf
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from tensorflow.compat.v1.keras.backend import set_session
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from tensorflow.keras.optimizers import SGD, Adam
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from tensorflow.keras.callbacks import ReduceLROnPlateau, EarlyStopping, Callback, ModelCheckpoint
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from sacred import Experiment
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from tensorflow.keras.models import load_model
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from tqdm import tqdm
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@ -61,6 +62,20 @@ class SaveWeightsAfterSteps(Callback):
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json.dump(self._config, fp) # encode dict into JSON
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print(f"saved model as steps {self.step_count} to {save_file}")
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def get_warmup_schedule(start_lr, target_lr, warmup_epochs, steps_per_epoch):
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initial_learning_rate = start_lr
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target_learning_rate = target_lr
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warmup_steps = warmup_epochs * steps_per_epoch
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lr_schedule = tf.keras.optimizers.schedules.LinearSchedule(
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initial_learning_rate=initial_learning_rate,
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final_learning_rate=target_learning_rate,
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total_steps=warmup_steps
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)
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return lr_schedule
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def configuration():
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config = tf.compat.v1.ConfigProto()
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@ -80,7 +95,6 @@ def get_dirs_or_files(input_data):
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ex = Experiment(save_git_info=False)
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@ex.config
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def config_params():
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n_classes = None # Number of classes. In the case of binary classification this should be 2.
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@ -145,6 +159,19 @@ def config_params():
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number_of_backgrounds_per_image = 1
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dir_rgb_backgrounds = None
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dir_rgb_foregrounds = None
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reduce_lr_enabled = False # Whether to use ReduceLROnPlateau callback
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reduce_lr_monitor = 'val_loss' # Metric to monitor for reducing learning rate
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reduce_lr_factor = 0.5 # Factor to reduce learning rate by
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reduce_lr_patience = 3 # Number of epochs to wait before reducing learning rate
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reduce_lr_min_lr = 1e-6 # Minimum learning rate
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reduce_lr_min_delta = 1e-5 # Minimum change in monitored value to be considered as improvement
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early_stopping_enabled = False # Whether to use EarlyStopping callback
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early_stopping_monitor = 'val_loss' # Metric to monitor for early stopping
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early_stopping_patience = 10 # Number of epochs to wait before stopping
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early_stopping_restore_best_weights = True # Whether to restore best weights when stopping
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warmup_enabled = False # Whether to use learning rate warmup
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warmup_epochs = 5 # Number of epochs for warmup
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warmup_start_lr = 1e-6 # Starting learning rate for warmup
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@ex.automain
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def run(_config, n_classes, n_epochs, input_height,
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@ -159,7 +186,10 @@ def run(_config, n_classes, n_epochs, input_height,
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transformer_mlp_head_units, transformer_layers, transformer_num_heads, transformer_cnn_first,
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transformer_patchsize_x, transformer_patchsize_y,
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transformer_num_patches_xy, backbone_type, save_interval, flip_index, dir_eval, dir_output,
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pretraining, learning_rate, task, f1_threshold_classification, classification_classes_name, dir_img_bin, number_of_backgrounds_per_image,dir_rgb_backgrounds, dir_rgb_foregrounds):
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pretraining, learning_rate, task, f1_threshold_classification, classification_classes_name, dir_img_bin, number_of_backgrounds_per_image,dir_rgb_backgrounds, dir_rgb_foregrounds,
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reduce_lr_enabled, reduce_lr_monitor, reduce_lr_factor, reduce_lr_patience, reduce_lr_min_lr, reduce_lr_min_delta,
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early_stopping_enabled, early_stopping_monitor, early_stopping_patience, early_stopping_restore_best_weights,
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warmup_enabled, warmup_epochs, warmup_start_lr):
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if dir_rgb_backgrounds:
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list_all_possible_background_images = os.listdir(dir_rgb_backgrounds)
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@ -320,20 +350,91 @@ def run(_config, n_classes, n_epochs, input_height,
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#if you want to see the model structure just uncomment model summary.
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model.summary()
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# Create callbacks list
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callbacks = []
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if reduce_lr_enabled:
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reduce_lr = ReduceLROnPlateau(
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monitor=reduce_lr_monitor,
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factor=reduce_lr_factor,
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patience=reduce_lr_patience,
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min_lr=reduce_lr_min_lr,
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min_delta=reduce_lr_min_delta,
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verbose=1
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)
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callbacks.append(reduce_lr)
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if early_stopping_enabled:
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early_stopping = EarlyStopping(
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monitor=early_stopping_monitor,
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patience=early_stopping_patience,
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restore_best_weights=early_stopping_restore_best_weights,
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verbose=1
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)
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callbacks.append(early_stopping)
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# Add checkpoint to save models every epoch
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class ModelCheckpointWithConfig(ModelCheckpoint):
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def __init__(self, *args, **kwargs):
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self._config = _config
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super().__init__(*args, **kwargs)
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def on_epoch_end(self, epoch, logs=None):
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super().on_epoch_end(epoch, logs)
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model_dir = os.path.join(dir_output, f"model_{epoch+1}")
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with open(os.path.join(model_dir, "config.json"), "w") as fp:
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json.dump(self._config, fp)
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checkpoint_epoch = ModelCheckpointWithConfig(
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os.path.join(dir_output, "model_{epoch}"),
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save_freq='epoch',
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save_weights_only=False,
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save_best_only=False,
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verbose=1
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)
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callbacks.append(checkpoint_epoch)
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# Calculate steps per epoch
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steps_per_epoch = int(len(os.listdir(dir_flow_train_imgs)) / n_batch) - 1
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# Create optimizer with or without warmup
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if warmup_enabled:
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lr_schedule = tf.keras.optimizers.schedules.PolynomialDecay(
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initial_learning_rate=warmup_start_lr,
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decay_steps=warmup_epochs * steps_per_epoch,
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end_learning_rate=learning_rate,
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power=1.0 # Linear decay
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)
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optimizer = Adam(learning_rate=lr_schedule)
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else:
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optimizer = Adam(learning_rate=learning_rate)
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if (task == "segmentation" or task == "binarization"):
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if not is_loss_soft_dice and not weighted_loss:
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model.compile(loss='categorical_crossentropy',
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optimizer=optimizer, metrics=['accuracy'])
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if is_loss_soft_dice:
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model.compile(loss=soft_dice_loss,
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optimizer=optimizer, metrics=['accuracy'])
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if weighted_loss:
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model.compile(loss=weighted_categorical_crossentropy(weights),
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optimizer=optimizer, metrics=['accuracy'])
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elif task == "enhancement":
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model.compile(loss='mean_squared_error',
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optimizer=optimizer, metrics=['accuracy'])
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if task == "segmentation" or task == "binarization":
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if not is_loss_soft_dice and not weighted_loss:
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model.compile(loss='categorical_crossentropy',
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optimizer=Adam(learning_rate=learning_rate), metrics=['accuracy'])
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optimizer=optimizer, metrics=['accuracy'])
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if is_loss_soft_dice:
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model.compile(loss=soft_dice_loss,
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optimizer=Adam(learning_rate=learning_rate), metrics=['accuracy'])
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optimizer=optimizer, metrics=['accuracy'])
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if weighted_loss:
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model.compile(loss=weighted_categorical_crossentropy(weights),
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optimizer=Adam(learning_rate=learning_rate), metrics=['accuracy'])
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optimizer=optimizer, metrics=['accuracy'])
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elif task == "enhancement":
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model.compile(loss='mean_squared_error',
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optimizer=Adam(learning_rate=learning_rate), metrics=['accuracy'])
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optimizer=optimizer, metrics=['accuracy'])
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# generating train and evaluation data
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@ -342,39 +443,22 @@ def run(_config, n_classes, n_epochs, input_height,
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val_gen = data_gen(dir_flow_eval_imgs, dir_flow_eval_labels, batch_size=n_batch,
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input_height=input_height, input_width=input_width, n_classes=n_classes, task=task)
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##img_validation_patches = os.listdir(dir_flow_eval_imgs)
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##score_best=[]
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##score_best.append(0)
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if save_interval:
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save_weights_callback = SaveWeightsAfterSteps(save_interval, dir_output, _config)
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for i in tqdm(range(index_start, n_epochs + index_start)):
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if save_interval:
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model.fit(
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# Single fit call with all epochs
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history = model.fit(
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train_gen,
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steps_per_epoch=int(len(os.listdir(dir_flow_train_imgs)) / n_batch) - 1,
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steps_per_epoch=steps_per_epoch,
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validation_data=val_gen,
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validation_steps=1,
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epochs=1, callbacks=[save_weights_callback])
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else:
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model.fit(
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train_gen,
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steps_per_epoch=int(len(os.listdir(dir_flow_train_imgs)) / n_batch) - 1,
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validation_data=val_gen,
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validation_steps=1,
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epochs=1)
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epochs=n_epochs,
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callbacks=callbacks
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)
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model.save(os.path.join(dir_output,'model_'+str(i)))
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# Save the best model (either from early stopping or final model)
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model.save(os.path.join(dir_output, 'model_best'))
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with open(os.path.join(os.path.join(dir_output,'model_'+str(i)),"config.json"), "w") as fp:
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with open(os.path.join(dir_output, 'model_best', "config.json"), "w") as fp:
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json.dump(_config, fp) # encode dict into JSON
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#os.system('rm -rf '+dir_train_flowing)
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#os.system('rm -rf '+dir_eval_flowing)
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#model.save(dir_output+'/'+'model'+'.h5')
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elif task=='classification':
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configuration()
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model = resnet50_classifier(n_classes, input_height, input_width, weight_decay, pretraining)
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53
train_no_patches_448x448.json
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train_no_patches_448x448.json
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@ -0,0 +1,53 @@
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{
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"backbone_type" : "nontransformer",
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"task": "segmentation",
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"n_classes" : 3,
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"n_epochs" : 50,
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"input_height" : 448,
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"input_width" : 448,
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"weight_decay" : 1e-4,
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"n_batch" : 4,
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"learning_rate": 2e-5,
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"patches" : false,
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"pretraining" : true,
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"augmentation" : true,
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"flip_aug" : false,
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"blur_aug" : false,
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"scaling" : true,
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"degrading": true,
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"brightening": false,
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"binarization" : false,
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"scaling_bluring" : false,
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"scaling_binarization" : false,
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"scaling_flip" : false,
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"rotation": false,
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"rotation_not_90": false,
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"blur_k" : ["blur","guass","median"],
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"scales" : [0.6, 0.7, 0.8, 0.9],
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"brightness" : [1.3, 1.5, 1.7, 2],
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"degrade_scales" : [0.2, 0.4],
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"flip_index" : [0, 1, -1],
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"thetha" : [10, -10],
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"continue_training": false,
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"index_start" : 0,
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"dir_of_start_model" : " ",
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"weighted_loss": false,
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"is_loss_soft_dice": true,
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"data_is_provided": true,
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"dir_train": "/home/incognito/sbb_pixelwise_segmentation/dataset/sam_41_mss/dir_train/train",
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"dir_eval": "/home/incognito/sbb_pixelwise_segmentation/dataset/sam_41_mss/dir_train/eval",
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"dir_output": "runs/sam_41_mss_npt_448x448",
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"reduce_lr_enabled": true,
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"reduce_lr_monitor": "val_loss",
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"reduce_lr_factor": 0.2,
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"reduce_lr_patience": 3,
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"reduce_lr_min_delta": 1e-5,
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"reduce_lr_min_lr": 1e-6,
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"early_stopping_enabled": true,
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"early_stopping_monitor": "val_loss",
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"early_stopping_patience": 6,
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"early_stopping_restore_best_weights": true,
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"warmup_enabled": true,
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"warmup_epochs": 5,
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"warmup_start_lr": 1e-6
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}
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