TrainingScripts/Train_2d_uncertaintyWeighting.py

import os, sys

currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir)  # PYTHON > 3.3 does not allow relative referencing

PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'

import numpy as np
import tensorflow as tf
from tensorflow.keras.callbacks import ModelCheckpoint, TensorBoard, EarlyStopping
import voxelmorph as vxm
import neurite as ne
import h5py
from datetime import datetime

import DeepDeformationMapRegistration.utils.constants as C
from DeepDeformationMapRegistration.data_generator import DataGeneratorManager2D
from DeepDeformationMapRegistration.utils.misc import try_mkdir
from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion
from DeepDeformationMapRegistration.layers import UncertaintyWeighting


os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER
os.environ['CUDA_VISIBLE_DEVICES'] = '1' # const.GPU_NUM  # Check availability before running using 'nvidia-smi'

C.TRAINING_DATASET = '/mnt/EncryptedData1/Users/javier/vessel_registration/ov_dataset/training'
C.BATCH_SIZE = 256
C.LIMIT_NUM_SAMPLES = None
C.EPOCHS = 10000

if PYCHARM_EXEC:
    path_prefix = os.path.join('scripts', 'tf')
else:
    path_prefix = ''

# Load data
# Build data generator
sample_list = [os.path.join(C.TRAINING_DATASET, f) for f in os.listdir(C.TRAINING_DATASET) if
               f.startswith('sample')]
sample_list.sort()

data_generator = DataGeneratorManager2D(sample_list[:C.LIMIT_NUM_SAMPLES],
                                        C.BATCH_SIZE, C.TRAINING_PERC,
                                        (64, 64, 1),
                                        fix_img_tag='dilated/input/fix',
                                        mov_img_tag='dilated/input/mov',
                                        multi_loss=True,
                                        )

# Build model
in_shape_img, in_shape_grad = data_generator.train_generator.input_shape
enc_features = [32, 32, 32, 32, 32, 32]  # const.ENCODER_FILTERS
dec_features = [32, 32, 32, 32, 32, 32, 32, 16]  # const.ENCODER_FILTERS[::-1]
nb_features = [enc_features, dec_features]
vxm_model = vxm.networks.VxmDense(inshape=in_shape_img[:-1], nb_unet_features=nb_features, int_steps=0)

#moving = tf.keras.Input(shape=in_shape_img, name='multiLoss_moving_input', dtype=tf.float32)
#fixed = tf.keras.Input(shape=in_shape_img, name='multiLoss_fixed_input', dtype=tf.float32)
grad = tf.keras.Input(shape=(*in_shape_img[:-1], 2), name='multiLoss_grad_input', dtype=tf.float32)

def dice_loss(y_true, y_pred):
    # Dice().loss returns -Dice score
    return 1 + vxm.losses.Dice().loss(y_true, y_pred)

#fixed_pred, dm_pred = vxm_model([moving, fixed])
multiLoss = UncertaintyWeighting(num_loss_fns=2,
                                 num_reg_fns=1,
                                 loss_fns=[HausdorffDistanceErosion(2, 2).loss, dice_loss],
                                 reg_fns=[vxm.losses.Grad('l2').loss],
                                 prior_loss_w=[1., 1.],
                                 prior_reg_w=[0.01],
                                 name='MultiLossLayer')
loss = multiLoss([vxm_model.inputs[1], vxm_model.inputs[1], vxm_model.references.y_source, vxm_model.references.y_source, grad, vxm_model.references.pos_flow])

full_model = tf.keras.Model(inputs=vxm_model.inputs + [grad], outputs=vxm_model.outputs + [loss])

# Compile the model
full_model.compile(optimizer=tf.keras.optimizers.Adam(lr=1e-4), loss=None)

# Train
output_folder = os.path.join('train_2d_multiloss_haussdorf_dice_grad' + datetime.now().strftime("%H%M%S-%d%m%Y"))
try_mkdir(output_folder)
try_mkdir(os.path.join(output_folder, 'checkpoints'))
try_mkdir(os.path.join(output_folder, 'tensorboard'))
my_callbacks = [
    # EarlyStopping(patience=const.EARLY_STOP_PATIENCE, monitor='dice', mode='max', verbose=1),
    ModelCheckpoint(os.path.join(output_folder, 'checkpoints', 'best_model.h5'),
                    save_best_only=True, monitor='val_loss', verbose=0, mode='min'),
    ModelCheckpoint(os.path.join(output_folder, 'checkpoints', 'weights.{epoch:05d}-{val_loss:.2f}.h5'),
                    save_best_only=True, save_weights_only=True, monitor='val_loss', verbose=0, mode='min'),
    # CSVLogger(train_log_name, ';'),
    # UpdateLossweights([haus_weight, dice_weight], [const.MODEL+'_resampler_seg', const.MODEL+'_resampler_seg'])
    TensorBoard(log_dir=os.path.join(output_folder, 'tensorboard'),
                batch_size=C.BATCH_SIZE, write_images=True, histogram_freq=10, update_freq='epoch',
                write_grads=True),
    EarlyStopping(monitor='val_loss', verbose=1, patience=50, min_delta=0.0001)
]
hist = full_model.fit_generator(data_generator.train_generator,
                                epochs=C.EPOCHS,
                                validation_data=data_generator.validation_generator,
                                verbose=2,
                                callbacks=my_callbacks)