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train_dl.py
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# -*- coding: utf-8 -*-
""" MEye: Semantic Segmentation """
import argparse
import os
os.sys.path += ['expman', 'models/deeplab']
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import math
import numpy as np
import pandas as pd
import tensorflow as tf
import tensorflowjs as tfjs
from tensorflow.keras import backend as K
from tensorflow.keras.models import load_model
from tensorflow.keras.callbacks import ModelCheckpoint, LearningRateScheduler, CSVLogger
from sklearn.model_selection import train_test_split
from sklearn.metrics import classification_report, roc_curve, auc, precision_recall_curve, average_precision_score
from adabelief_tf import AdaBeliefOptimizer
from tqdm.keras import TqdmCallback
from tqdm import tqdm
from functools import partial
from dataloader import get_loader, load_datasets
from deeplabv3p.models.deeplabv3p_mobilenetv3 import hard_swish
from models.deeplab import build_model, AVAILABLE_BACKBONES
from utils import visualize
from expman import Experiment
import evaluate
def main(args):
exp = Experiment(args, ignore=('epochs', 'resume'))
print(exp)
np.random.seed(args.seed)
tf.random.set_seed(args.seed)
data = load_datasets(args.data)
# TRAIN/VAL/TEST SPLIT
if args.split == 'subjects': # by SUBJECTS
val_subjects = (6, 9, 11, 13, 16, 28, 30, 48, 49)
test_subjects = (3, 4, 19, 38, 45, 46, 51, 52)
train_data = data[~data['sub'].isin(val_subjects + test_subjects)]
val_data = data[data['sub'].isin(val_subjects)]
test_data = data[data['sub'].isin(test_subjects)]
elif args.split == 'random': # 70-20-10 %
train_data, valtest_data = train_test_split(data, test_size=.3, shuffle=True)
val_data, test_data = train_test_split(valtest_data, test_size=.33)
lengths = map(len, (data, train_data, val_data, test_data))
print("Total: {} - Train / Val / Test: {} / {} / {}".format(*lengths))
x_shape = (args.resolution, args.resolution, 1)
y_shape = (args.resolution, args.resolution, 1)
train_gen, _ = get_loader(train_data, batch_size=args.batch_size, shuffle=True, augment=True, x_shape=x_shape)
val_gen, val_categories = get_loader(val_data, batch_size=args.batch_size, x_shape=x_shape)
# test_gen, test_categories = get_loader(test_data, batch_size=1, x_shape=x_shape)
log = exp.path_to('log.csv')
# weights_only checkpoints
best_weights_path = exp.path_to('best_weights.h5')
best_mask_weights_path = exp.path_to('best_weights_mask.h5')
# whole model checkpoints
best_ckpt_path = exp.path_to('best_model.h5')
last_ckpt_path = exp.path_to('last_model.h5')
if args.resume and os.path.exists(last_ckpt_path):
custom_objects={'AdaBeliefOptimizer': AdaBeliefOptimizer, 'iou_coef': evaluate.iou_coef, 'dice_coef': evaluate.dice_coef, 'hard_swish': hard_swish}
model = tf.keras.models.load_model(last_ckpt_path, custom_objects=custom_objects)
optimizer = model.optimizer
initial_epoch = len(pd.read_csv(log))
else:
config = vars(args)
model = build_model(x_shape, y_shape, config)
optimizer = AdaBeliefOptimizer(learning_rate=args.lr, print_change_log=False)
initial_epoch = 0
model.compile(optimizer=optimizer,
loss='binary_crossentropy',
metrics={'mask': [evaluate.iou_coef, evaluate.dice_coef],
'tags': 'binary_accuracy'})
model_stopped_file = exp.path_to('early_stopped.txt')
need_training = not os.path.exists(model_stopped_file) and initial_epoch < args.epochs
if need_training:
best_checkpointer = ModelCheckpoint(best_weights_path, monitor='val_loss', save_best_only=True, save_weights_only=True)
best_mask_checkpointer = ModelCheckpoint(best_mask_weights_path, monitor='val_mask_dice_coef', mode='max', save_best_only=True, save_weights_only=True)
last_checkpointer = ModelCheckpoint(last_ckpt_path, save_best_only=False, save_weights_only=False)
logger = CSVLogger(log, append=args.resume)
progress = TqdmCallback(verbose=1, initial=initial_epoch, dynamic_ncols=True)
early_stop = tf.keras.callbacks.EarlyStopping(monitor='val_mask_dice_coef', mode='max', patience=100)
callbacks = [best_checkpointer, best_mask_checkpointer, last_checkpointer, logger, progress, early_stop]
model.fit(train_gen,
epochs=args.epochs,
callbacks=callbacks,
initial_epoch=initial_epoch,
steps_per_epoch=len(train_gen),
validation_data=val_gen,
validation_steps=len(val_gen),
verbose=False)
if model.stop_training:
open(model_stopped_file, 'w').close()
tf.keras.models.save_model(model, best_ckpt_path, include_optimizer=False)
# evaluation on test set
evaluate.evaluate(exp, force=need_training)
# save best snapshot in SavedModel format
model.load_weights(best_mask_weights_path)
best_savedmodel_path = exp.path_to('best_savedmodel')
model.save(best_savedmodel_path, save_traces=True)
# export to tfjs (Layers model)
tfjs_model_dir = exp.path_to('tfjs')
tfjs.converters.save_keras_model(model, tfjs_model_dir)
if __name__ == '__main__':
default_data = ['data/NN_human_mouse_eyes']
parser = argparse.ArgumentParser(description='Train DeepLab models')
# data params
parser.add_argument('-d', '--data', nargs='+', default=default_data, help='Data directory (may be multiple)')
parser.add_argument('--split', default='random', choices=('random', 'subjects'), help='How to split data')
parser.add_argument('-r', '--resolution', type=int, default=128, help='Input image resolution')
# model params
parser.add_argument('-a', '--backbone', default='resnet50', choices=AVAILABLE_BACKBONES, help='Backbone architecture')
# train params
parser.add_argument('--lr', type=float, default=0.001, help='learning rate')
parser.add_argument('-b', '--batch-size', type=int, default=32, help='Batch size')
parser.add_argument('-e', '--epochs', type=int, default=500, help='Number of training epochs')
parser.add_argument('-s', '--seed', type=int, default=23, help='Random seed')
parser.add_argument('--resume', default=False, action='store_true', help='Resume training')
args = parser.parse_args()
main(args)