a b/fetal/experiments/train_semi.py
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import glob
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import os
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import keras.backend as K
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import numpy as np
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from keras import Input, Model
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from keras.engine.network import Network
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from keras.layers import Activation, Concatenate
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from keras.optimizers import Adam
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from tqdm import tqdm
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import fetal_net
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import fetal_net.metrics
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import fetal_net.preprocess
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from fetal.config_utils import get_config
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from fetal.utils import get_last_model_path, create_data_file, set_gpu_mem_growth
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from fetal_net.data import open_data_file
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from fetal_net.generator import get_training_and_validation_generators
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from fetal_net.model.fetal_net import fetal_envelope_model
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set_gpu_mem_growth()
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config = get_config()
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if not "dis_model_name" in config:
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    config["dis_model_name"] = "discriminator_image"
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if not "dis_loss" in config:
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    config["dis_loss"] = "binary_crossentropy_loss"
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if not "gen_steps" in config:
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    config["gen_steps"] = 1
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if not "dis_steps" in config:
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    config["dis_steps"] = 1
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if not "gd_loss_ratio" in config:
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    config["gd_loss_ratio"] = 10
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class Scheduler:
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    def __init__(self, n_itrs_per_epoch_d, n_itrs_per_epoch_g, init_lr, lr_decay, lr_patience):
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        self.init_dsteps = n_itrs_per_epoch_d
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        self.init_gsteps = n_itrs_per_epoch_g
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        self.init_lr = init_lr
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        self.lr_decay = lr_decay
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        self.lr_patience = lr_patience
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        self.dsteps = self.init_dsteps
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        self.gsteps = self.init_gsteps
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        self.lr = self.init_lr
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        self.steps_stuck = 0
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        self.best_loss = np.inf
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    def get_dsteps(self):
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        return self.dsteps
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    def get_gsteps(self):
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        return self.gsteps
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    def get_lr(self):
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        return self.lr
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    def update_steps(self, n_round, loss):
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        if loss < self.best_loss:
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            self.steps_stuck = 0
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            self.best_loss = loss
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        else:
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            self.steps_stuck += 1
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        if self.steps_stuck > self.lr_patience:
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            self.lr *= self.lr_decay
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            self.steps_stuck = 0
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            print('Reducing LR to {}'.format(self.lr))
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        # if key in self.schedules['step_decay']:
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        # self.dsteps = max(int(self.init_dsteps * self.schedules['step_decay'][key]), 1)
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        # self.gsteps = max(int(self.init_gsteps * self.schedules['step_decay'][key]), 1)
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def build_dsc(out_labels, outs):
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    s = ''
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    for l, o in zip(out_labels, outs):
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        s = s + '{}={:.3f}, '.format(l, o)
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    return s[:-2] + '|'
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def add_noise_to_segs(segs):
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    if np.random.choice([True, False]):
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        segs = segs.astype(np.float32)
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        segs += np.random.normal(0, 0.025, segs.shape)
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        segs *= np.random.normal(1, 0.025, segs.shape)
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        segs = np.clip(segs, a_min=0, a_max=1)
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    return segs
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def mul_merge_maps(r, s):
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    r_plus = r * s
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    r_minus = r * (1 - s)
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    return np.concatenate((r_plus, r_minus), axis=1)
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def input2discriminator(real_patches, real_segs, semi_patches, semi_segs, d_out_shape, mul_merge=True):
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    if mul_merge:
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        real = mul_merge_maps(real_patches, add_noise_to_segs(real_segs))
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        fake = mul_merge_maps(semi_patches, semi_segs)
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    else:
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        real = np.concatenate((real_patches, add_noise_to_segs(real_segs)), axis=1)
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        fake = np.concatenate((semi_patches, semi_segs), axis=1)
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    d_x_batch = np.concatenate((real, fake), axis=0)
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    # real : 1, fake : 0
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    d_y_batch = np.clip(np.random.uniform(0.9, 1.0, size=[d_x_batch.shape[0]] + list(d_out_shape)[1:]),
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                        a_min=0, a_max=1)
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    d_y_batch[real.shape[0]:, ...] = 1 - d_y_batch[real.shape[0]:, ...]
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    return d_x_batch, d_y_batch
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def input2gan(real_patches, real_segs, semi_patches, d_out_shape):
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    g_x_batch = [real_patches, semi_patches]
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    # set 1 to all labels (real : 1, fake : 0)
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    g_y_batch = [
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        real_segs,
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        np.clip(np.random.uniform(0.9, 1.0, size=[real_patches.shape[0]] + list(d_out_shape)[1:]), a_min=0, a_max=1)
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    ]
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    return g_x_batch, g_y_batch
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def main(overwrite=False):
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    # convert input images into an hdf5 file
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    if overwrite or not os.path.exists(config["data_file"]):
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        create_data_file(config)
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    data_file_opened = open_data_file(config["data_file"])
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    seg_loss_func = getattr(fetal_net.metrics, config['loss'])
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    dis_loss_func = getattr(fetal_net.metrics, config['dis_loss'])
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    # instantiate new model
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    seg_model_func = getattr(fetal_net.model, config['model_name'])
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    gen_model = seg_model_func(input_shape=config["input_shape"],
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                               initial_learning_rate=config["initial_learning_rate"],
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                               **{'dropout_rate': config['dropout_rate'],
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                                  'loss_function': seg_loss_func,
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                                  'mask_shape': None if config["weight_mask"] is None else config[
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                                      "input_shape"],
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                                  'old_model_path': config['old_model']})
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    dis_model_func = getattr(fetal_net.model, config['dis_model_name'])
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    dis_model = dis_model_func(
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        input_shape=[config["input_shape"][0] + config["n_labels"]] + config["input_shape"][1:],
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        initial_learning_rate=config["initial_learning_rate"],
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        **{'dropout_rate': config['dropout_rate'],
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           'loss_function': dis_loss_func})
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    if not overwrite \
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            and len(glob.glob(config["model_file"] + 'g_*.h5')) > 0:
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        # dis_model_path = get_last_model_path(config["model_file"] + 'dis_')
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        gen_model_path = get_last_model_path(config["model_file"] + 'g_')
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        # print('Loading dis model from: {}'.format(dis_model_path))
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        print('Loading gen model from: {}'.format(gen_model_path))
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        # dis_model = load_old_model(dis_model_path)
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        # gen_model = load_old_model(gen_model_path)
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        # dis_model.load_weights(dis_model_path)
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        gen_model.load_weights(gen_model_path)
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    gen_model.summary()
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    dis_model.summary()
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    # Build "frozen discriminator"
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    frozen_dis_model = Network(
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        dis_model.inputs,
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        dis_model.outputs,
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        name='frozen_discriminator'
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    )
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    frozen_dis_model.trainable = False
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    inputs_real = Input(shape=config["input_shape"])
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    inputs_fake = Input(shape=config["input_shape"])
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    segs_real = Activation(None, name='seg_real')(gen_model(inputs_real))
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    segs_fake = Activation(None, name='seg_fake')(gen_model(inputs_fake))
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    valid = Activation(None, name='dis')(frozen_dis_model(Concatenate(axis=1)([segs_fake, inputs_fake])))
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    combined_model = Model(inputs=[inputs_real, inputs_fake],
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                           outputs=[segs_real, valid])
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    combined_model.compile(loss=[seg_loss_func, 'binary_crossentropy'],
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                           loss_weights=[1, config["gd_loss_ratio"]],
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                           optimizer=Adam(config["initial_learning_rate"]))
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    combined_model.summary()
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    # get training and testing generators
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    train_generator, validation_generator, n_train_steps, n_validation_steps = get_training_and_validation_generators(
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        data_file_opened,
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        batch_size=config["batch_size"],
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        data_split=config["validation_split"],
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        overwrite=overwrite,
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        validation_keys_file=config["validation_file"],
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        training_keys_file=config["training_file"],
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        test_keys_file=config["test_file"],
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        n_labels=config["n_labels"],
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        labels=config["labels"],
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        patch_shape=(*config["patch_shape"], config["patch_depth"]),
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        validation_batch_size=config["validation_batch_size"],
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        augment=config["augment"],
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        skip_blank_train=config["skip_blank_train"],
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        skip_blank_val=config["skip_blank_val"],
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        truth_index=config["truth_index"],
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        truth_size=config["truth_size"],
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        prev_truth_index=config["prev_truth_index"],
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        prev_truth_size=config["prev_truth_size"],
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        truth_downsample=config["truth_downsample"],
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        truth_crop=config["truth_crop"],
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        patches_per_epoch=config["patches_per_epoch"],
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        categorical=config["categorical"], is3d=config["3D"],
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        drop_easy_patches_train=config["drop_easy_patches_train"],
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        drop_easy_patches_val=config["drop_easy_patches_val"])
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    # get training and testing generators
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    _, semi_generator, _, _ = get_training_and_validation_generators(
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        data_file_opened,
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        batch_size=config["batch_size"],
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        data_split=config["validation_split"],
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        overwrite=overwrite,
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        validation_keys_file=config["validation_file"],
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        training_keys_file=config["training_file"],
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        test_keys_file=config["test_file"],
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        n_labels=config["n_labels"],
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        labels=config["labels"],
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        patch_shape=(*config["patch_shape"], config["patch_depth"]),
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        validation_batch_size=config["validation_batch_size"],
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        val_augment=config["augment"],
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        skip_blank_train=config["skip_blank_train"],
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        skip_blank_val=config["skip_blank_val"],
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        truth_index=config["truth_index"],
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        truth_size=config["truth_size"],
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        prev_truth_index=config["prev_truth_index"],
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        prev_truth_size=config["prev_truth_size"],
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        truth_downsample=config["truth_downsample"],
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        truth_crop=config["truth_crop"],
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        patches_per_epoch=config["patches_per_epoch"],
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        categorical=config["categorical"], is3d=config["3D"],
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        drop_easy_patches_train=config["drop_easy_patches_train"],
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        drop_easy_patches_val=config["drop_easy_patches_val"])
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    # start training
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    scheduler = Scheduler(config["dis_steps"], config["gen_steps"],
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                          init_lr=config["initial_learning_rate"],
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                          lr_patience=config["patience"],
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                          lr_decay=config["learning_rate_drop"])
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    best_loss = np.inf
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    for epoch in range(config["n_epochs"]):
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        postfix = {'g': None, 'd': None}  # , 'val_g': None, 'val_d': None}
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        with tqdm(range(n_train_steps // config["gen_steps"]), dynamic_ncols=True,
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                  postfix={'gen': None, 'dis': None, 'val_gen': None, 'val_dis': None, None: None}) as pbar:
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            for n_round in pbar:
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                # train D
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                outputs = np.zeros(dis_model.metrics_names.__len__())
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                for i in range(scheduler.get_dsteps()):
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                    real_patches, real_segs = next(train_generator)
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                    semi_patches, _ = next(semi_generator)
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                    d_x_batch, d_y_batch = input2discriminator(real_patches, real_segs,
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                                                               semi_patches,
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                                                               gen_model.predict(semi_patches,
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                                                                                 batch_size=config["batch_size"]),
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                                                               dis_model.output_shape)
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                    outputs += dis_model.train_on_batch(d_x_batch, d_y_batch)
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                if scheduler.get_dsteps():
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                    outputs /= scheduler.get_dsteps()
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                    postfix['d'] = build_dsc(dis_model.metrics_names, outputs)
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                    pbar.set_postfix(**postfix)
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                # train G (freeze discriminator)
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                outputs = np.zeros(combined_model.metrics_names.__len__())
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                for i in range(scheduler.get_gsteps()):
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                    real_patches, real_segs = next(train_generator)
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                    semi_patches, _ = next(validation_generator)
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                    g_x_batch, g_y_batch = input2gan(real_patches, real_segs, semi_patches, dis_model.output_shape)
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                    outputs += combined_model.train_on_batch(g_x_batch, g_y_batch)
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                outputs /= scheduler.get_gsteps()
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                postfix['g'] = build_dsc(combined_model.metrics_names, outputs)
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                pbar.set_postfix(**postfix)
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            # evaluate on validation set
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            dis_metrics = np.zeros(dis_model.metrics_names.__len__(), dtype=float)
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            gen_metrics = np.zeros(gen_model.metrics_names.__len__(), dtype=float)
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            evaluation_rounds = n_validation_steps
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            for n_round in range(evaluation_rounds):  # rounds_for_evaluation:
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                val_patches, val_segs = next(validation_generator)
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                # D
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                if scheduler.get_dsteps() > 0:
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                    d_x_test, d_y_test = input2discriminator(val_patches, val_segs,
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                                                             val_patches,
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                                                             gen_model.predict(val_patches,
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                                                                               batch_size=config[
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                                                                                   "validation_batch_size"]),
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                                                             dis_model.output_shape)
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                    dis_metrics += dis_model.evaluate(d_x_test, d_y_test, batch_size=config["validation_batch_size"],
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                                                      verbose=0)
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                # G
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                # gen_x_test, gen_y_test = input2gan(val_patches, val_segs, dis_model.output_shape)
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                gen_metrics += gen_model.evaluate(val_patches, val_segs,
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                                                  batch_size=config["validation_batch_size"],
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                                                  verbose=0)
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            dis_metrics /= float(evaluation_rounds)
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            gen_metrics /= float(evaluation_rounds)
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            # save the model and weights with the best validation loss
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            if gen_metrics[0] < best_loss:
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                best_loss = gen_metrics[0]
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                print('Saving Model...')
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                with open(os.path.join(config["base_dir"], "g_{}_{:.3f}.json".format(epoch, gen_metrics[0])),
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                          'w') as f:
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                    f.write(gen_model.to_json())
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                gen_model.save_weights(
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                    os.path.join(config["base_dir"], "g_{}_{:.3f}.h5".format(epoch, gen_metrics[0])))
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            postfix['val_d'] = build_dsc(dis_model.metrics_names, dis_metrics)
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            postfix['val_g'] = build_dsc(gen_model.metrics_names, gen_metrics)
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            # pbar.set_postfix(**postfix)
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            print('val_d: ' + postfix['val_d'], end=' | ')
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            print('val_g: ' + postfix['val_g'])
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            # pbar.refresh()
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            # update step sizes, learning rates
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            scheduler.update_steps(epoch, gen_metrics[0])
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            K.set_value(dis_model.optimizer.lr, scheduler.get_lr())
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            K.set_value(combined_model.optimizer.lr, scheduler.get_lr())
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    data_file_opened.close()
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if __name__ == "__main__":
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    main(overwrite=config["overwrite"])