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b/scripts/train.py |
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#!/usr/bin/env python |
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from __future__ import division, print_function |
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import os |
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import argparse |
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import logging |
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from keras import losses, optimizers, utils |
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from keras.optimizers import SGD, RMSprop, Adagrad, Adadelta, Adam, Adamax, Nadam |
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from keras.callbacks import ModelCheckpoint |
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from keras import backend as K |
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from rvseg import dataset, models, loss, opts |
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def select_optimizer(optimizer_name, optimizer_args): |
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optimizers = { |
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'sgd': SGD, |
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'rmsprop': RMSprop, |
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'adagrad': Adagrad, |
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'adadelta': Adadelta, |
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'adam': Adam, |
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'adamax': Adamax, |
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'nadam': Nadam, |
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} |
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if optimizer_name not in optimizers: |
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raise Exception("Unknown optimizer ({}).".format(name)) |
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return optimizers[optimizer_name](**optimizer_args) |
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def train(): |
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logging.basicConfig(level=logging.INFO) |
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args = opts.parse_arguments() |
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logging.info("Loading dataset...") |
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augmentation_args = { |
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'rotation_range': args.rotation_range, |
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'width_shift_range': args.width_shift_range, |
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'height_shift_range': args.height_shift_range, |
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'shear_range': args.shear_range, |
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'zoom_range': args.zoom_range, |
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'fill_mode' : args.fill_mode, |
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'alpha': args.alpha, |
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'sigma': args.sigma, |
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} |
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train_generator, train_steps_per_epoch, \ |
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val_generator, val_steps_per_epoch = dataset.create_generators( |
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args.datadir, args.batch_size, |
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validation_split=args.validation_split, |
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mask=args.classes, |
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shuffle_train_val=args.shuffle_train_val, |
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shuffle=args.shuffle, |
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seed=args.seed, |
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normalize_images=args.normalize, |
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augment_training=args.augment_training, |
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augment_validation=args.augment_validation, |
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augmentation_args=augmentation_args) |
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# get image dimensions from first batch |
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images, masks = next(train_generator) |
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_, height, width, channels = images.shape |
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_, _, _, classes = masks.shape |
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logging.info("Building model...") |
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string_to_model = { |
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"unet": models.unet, |
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"dilated-unet": models.dilated_unet, |
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"dilated-densenet": models.dilated_densenet, |
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"dilated-densenet2": models.dilated_densenet2, |
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"dilated-densenet3": models.dilated_densenet3, |
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} |
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model = string_to_model[args.model] |
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m = model(height=height, width=width, channels=channels, classes=classes, |
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features=args.features, depth=args.depth, padding=args.padding, |
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temperature=args.temperature, batchnorm=args.batchnorm, |
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dropout=args.dropout) |
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m.summary() |
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if args.load_weights: |
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logging.info("Loading saved weights from file: {}".format(args.load_weights)) |
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m.load_weights(args.load_weights) |
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# instantiate optimizer, and only keep args that have been set |
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# (not all optimizers have args like `momentum' or `decay') |
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optimizer_args = { |
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'lr': args.learning_rate, |
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'momentum': args.momentum, |
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'decay': args.decay |
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} |
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for k in list(optimizer_args): |
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if optimizer_args[k] is None: |
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del optimizer_args[k] |
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optimizer = select_optimizer(args.optimizer, optimizer_args) |
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# select loss function: pixel-wise crossentropy, soft dice or soft |
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# jaccard coefficient |
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if args.loss == 'pixel': |
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def lossfunc(y_true, y_pred): |
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return loss.weighted_categorical_crossentropy( |
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y_true, y_pred, args.loss_weights) |
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elif args.loss == 'dice': |
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def lossfunc(y_true, y_pred): |
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return loss.sorensen_dice_loss(y_true, y_pred, args.loss_weights) |
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elif args.loss == 'jaccard': |
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def lossfunc(y_true, y_pred): |
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return loss.jaccard_loss(y_true, y_pred, args.loss_weights) |
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else: |
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raise Exception("Unknown loss ({})".format(args.loss)) |
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def dice(y_true, y_pred): |
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batch_dice_coefs = loss.sorensen_dice(y_true, y_pred, axis=[1, 2]) |
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dice_coefs = K.mean(batch_dice_coefs, axis=0) |
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return dice_coefs[1] # HACK for 2-class case |
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def jaccard(y_true, y_pred): |
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batch_jaccard_coefs = loss.jaccard(y_true, y_pred, axis=[1, 2]) |
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jaccard_coefs = K.mean(batch_jaccard_coefs, axis=0) |
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return jaccard_coefs[1] # HACK for 2-class case |
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metrics = ['accuracy', dice, jaccard] |
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m.compile(optimizer=optimizer, loss=lossfunc, metrics=metrics) |
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# automatic saving of model during training |
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if args.checkpoint: |
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if args.loss == 'pixel': |
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filepath = os.path.join( |
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args.outdir, "weights-{epoch:02d}-{val_acc:.4f}.hdf5") |
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monitor = 'val_acc' |
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mode = 'max' |
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elif args.loss == 'dice': |
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filepath = os.path.join( |
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args.outdir, "weights-{epoch:02d}-{val_dice:.4f}.hdf5") |
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monitor='val_dice' |
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mode = 'max' |
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elif args.loss == 'jaccard': |
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filepath = os.path.join( |
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args.outdir, "weights-{epoch:02d}-{val_jaccard:.4f}.hdf5") |
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monitor='val_jaccard' |
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mode = 'max' |
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checkpoint = ModelCheckpoint( |
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filepath, monitor=monitor, verbose=1, |
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save_best_only=True, mode=mode) |
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callbacks = [checkpoint] |
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else: |
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callbacks = [] |
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# train |
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logging.info("Begin training.") |
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m.fit_generator(train_generator, |
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epochs=args.epochs, |
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steps_per_epoch=train_steps_per_epoch, |
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validation_data=val_generator, |
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validation_steps=val_steps_per_epoch, |
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callbacks=callbacks, |
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verbose=2) |
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m.save(os.path.join(args.outdir, args.outfile)) |
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if __name__ == '__main__': |
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train() |