--- a
+++ b/3D/train.py
@@ -0,0 +1,147 @@
+
+from __future__ import print_function
+
+# import packages
+from model import unet_model_3d
+from keras.utils import plot_model
+from keras import callbacks
+from keras.callbacks import ModelCheckpoint, CSVLogger, LearningRateScheduler, ReduceLROnPlateau, EarlyStopping
+
+# import load data
+from data_handling import load_train_data, load_validatation_data
+
+# import configurations
+import configs
+
+# init configs
+patch_size = configs.PATCH_SIZE
+batch_size = configs.BATCH_SIZE
+
+config = dict()
+config["pool_size"] = (2, 2, 2)  # pool size for the max pooling operations
+config["image_shape"] = (256, 128, 256)  # This determines what shape the images will be cropped/resampled to.
+config["input_shape"] = (patch_size, patch_size, patch_size, 1)  # switch to None to train on the whole image (64, 64, 64) (64, 64, 64)
+config["n_labels"] = 4
+config["all_modalities"] = ['t1']#]["t1", "t1Gd", "flair", "t2"]
+config["training_modalities"] = config["all_modalities"]  # change this if you want to only use some of the modalities
+config["nb_channels"] = len(config["training_modalities"])
+config["deconvolution"] = False  # if False, will use upsampling instead of deconvolution
+config["batch_size"] = batch_size
+config["n_epochs"] = 500  # cutoff the training after this many epochs
+config["patience"] = 10  # learning rate will be reduced after this many epochs if the validation loss is not improving
+config["early_stop"] = 31  # training will be stopped after this many epochs without the validation loss improving
+config["initial_learning_rate"] = 0.0001
+config["depth"] = configs.DEPTH
+config["learning_rate_drop"] = 0.5
+
+image_type = '3d_patches'
+
+# 3D U-net depth=5
+def generate_model(num_classes=4) :
+    init_input = Input((1, 32, 32, 32))
+
+    x = Conv3D(25, kernel_size=(3, 3, 3))(init_input)
+    x = PReLU()(x)
+    x = Conv3D(25, kernel_size=(3, 3, 3))(x)
+    x = PReLU()(x)
+    x = Conv3D(25, kernel_size=(3, 3, 3))(x)
+    x = PReLU()(x)
+
+    y = Conv3D(50, kernel_size=(3, 3, 3))(x)
+    y = PReLU()(y)
+    y = Conv3D(50, kernel_size=(3, 3, 3))(y)
+    y = PReLU()(y)
+    y = Conv3D(50, kernel_size=(3, 3, 3))(y)
+    y = PReLU()(y)
+
+    z = Conv3D(75, kernel_size=(3, 3, 3))(y)
+    z = PReLU()(z)
+    z = Conv3D(75, kernel_size=(3, 3, 3))(z)
+    z = PReLU()(z)
+    z = Conv3D(75, kernel_size=(3, 3, 3))(z)
+    z = PReLU()(z)
+
+    x_crop = Cropping3D(cropping=((6, 6), (6, 6), (6, 6)))(x)
+    y_crop = Cropping3D(cropping=((3, 3), (3, 3), (3, 3)))(y)
+
+    concat = concatenate([x_crop, y_crop, z], axis=1)
+
+    fc = Conv3D(400, kernel_size=(1, 1, 1))(concat)
+    fc = PReLU()(fc)
+    fc = Conv3D(200, kernel_size=(1, 1, 1))(fc)
+    fc = PReLU()(fc)
+    fc = Conv3D(150, kernel_size=(1, 1, 1))(fc)
+    fc = PReLU()(fc)
+
+    pred = Conv3D(num_classes, kernel_size=(1, 1, 1))(fc)
+    pred = PReLU()(pred)
+    pred = Reshape((num_classes, 9 * 9 * 9))(pred)
+    pred = Permute((2, 1))(pred)
+    pred = Activation('softmax')(pred)
+
+    model = Model(inputs=init_input, outputs=pred)
+    model.compile(
+        loss='categorical_crossentropy',
+        optimizer='adam',
+        metrics=['categorical_accuracy'])
+    return model
+
+# train
+def train():
+    print('-'*30)
+    print('Loading and preprocessing train data...')
+    print('-'*30)
+    imgs_train, imgs_gtruth_train = load_train_data()
+    
+    print('-'*30)
+    print('Loading and preprocessing validation data...')
+    print('-'*30)
+    imgs_val, imgs_gtruth_val  = load_validatation_data()
+    
+    print('-'*30)
+    print('Creating and compiling model...')
+    print('-'*30)
+
+   # create a model
+    model = unet_model_3d(input_shape=config["input_shape"],
+                                depth=config["depth"],
+                                pool_size=config["pool_size"],
+                                n_labels=config["n_labels"],
+                                initial_learning_rate=config["initial_learning_rate"],
+                                deconvolution=config["deconvolution"])
+
+    model.summary()
+    
+    print('-'*30)
+    print('Fitting model...')
+    print('-'*30)
+    
+    #============================================================================
+    print('training starting..')
+    log_filename = 'outputs/' + image_type +'_model_train.csv' 
+    
+    
+    csv_log = callbacks.CSVLogger(log_filename, separator=',', append=True)
+    
+#    early_stopping = callbacks.EarlyStopping(monitor='val_loss', min_delta=0, patience=5, verbose=0, mode='min')
+    
+    #checkpoint_filepath = 'outputs/' + image_type +"_best_weight_model_{epoch:03d}_{val_loss:.4f}.hdf5"
+    checkpoint_filepath = 'outputs/' + 'weights.h5'
+    
+    checkpoint = callbacks.ModelCheckpoint(checkpoint_filepath, monitor='val_loss', verbose=1, save_best_only=True, mode='min')
+    
+    callbacks_list = [csv_log, checkpoint]
+    callbacks_list.append(ReduceLROnPlateau(factor=config["learning_rate_drop"], patience=config["patience"],
+                                           verbose=True))
+    callbacks_list.append(EarlyStopping(verbose=True, patience=config["early_stop"]))
+
+    #============================================================================
+    hist = model.fit(imgs_train, imgs_gtruth_train, batch_size=config["batch_size"], nb_epoch=config["n_epochs"], verbose=1, validation_data=(imgs_val,imgs_gtruth_val), shuffle=True, callbacks=callbacks_list) #              validation_split=0.2,
+        
+     
+    model_name = 'outputs/' + image_type + '_model_last'
+    model.save(model_name)  # creates a HDF5 file 'my_model.h5'
+
+# main  
+if __name__ == '__main__':
+    train()