deepreg.train.main() - Code Metrics - Inspection of "734 large dice" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#736)

by Yunguan

created 2021-04-04 01:24 UTC

deepreg.train.main() B

↳ Parent: deepreg.train

Complexity

Conditions

Size

Total Lines	76
Code Lines	49

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	49
dl	0
loc	76
rs	8.669
c	0
b	0
f	0
cc	1
nop	1

How to fix Long Method

# coding=utf-8

"""
Module to train a network using init files and a CLI.
"""

import argparse
import os
from typing import Dict, List, Tuple, Union

import tensorflow as tf

import deepreg.config.parser as config_parser
import deepreg.model.optimizer as opt
from deepreg.callback import build_checkpoint_callback
from deepreg.registry import REGISTRY
from deepreg.util import build_dataset, build_log_dir


def build_config(
    config_path: Union[str, List[str]],
    log_dir: str,
    exp_name: str,
    ckpt_path: str,
    max_epochs: int = -1,
) -> Tuple[Dict, str, str]:
    """
    Function to initialise log directories,
    assert that checkpointed model is the right
    type and to parse the configuration for training.

    :param config_path: list of str, path to config file
    :param log_dir: path of the log directory
    :param exp_name: name of the experiment
    :param ckpt_path: path where model is stored.
    :param max_epochs: if max_epochs > 0, use it to overwrite the configuration
    :return: - config: a dictionary saving configuration
             - exp_name: the path of directory to save logs
    """

    # init log directory
    log_dir = build_log_dir(log_dir=log_dir, exp_name=exp_name)

    # load config
    config = config_parser.load_configs(config_path)

    # replace the ~ with user home path
    ckpt_path = os.path.expanduser(ckpt_path)

    # overwrite epochs and save_period if necessary
    if max_epochs > 0:
        config["train"]["epochs"] = max_epochs
        config["train"]["save_period"] = min(max_epochs, config["train"]["save_period"])

    # backup config
    config_parser.save(config=config, out_dir=log_dir)

    return config, log_dir, ckpt_path


def train(
    gpu: str,
    config_path: Union[str, List[str]],
    gpu_allow_growth: bool,
    ckpt_path: str,
    exp_name: str = "",
    log_dir: str = "logs",
    max_epochs: int = -1,
):
    """
    Function to train a model.

    :param gpu: which local gpu to use to train.
    :param config_path: path to configuration set up.
    :param gpu_allow_growth: whether to allocate whole GPU memory for training.
    :param ckpt_path: where to store training checkpoints.
    :param log_dir: path of the log directory.
    :param exp_name: experiment name.
    :param max_epochs: if max_epochs > 0, will use it to overwrite the configuration.
    """
    # set env variables
    os.environ["CUDA_VISIBLE_DEVICES"] = gpu
    os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "true" if gpu_allow_growth else "false"

    # load config
    config, log_dir, ckpt_path = build_config(
        config_path=config_path,
        log_dir=log_dir,
        exp_name=exp_name,
        ckpt_path=ckpt_path,
        max_epochs=max_epochs,
    )

    # build dataset
    data_loader_train, dataset_train, steps_per_epoch_train = build_dataset(
        dataset_config=config["dataset"],
        preprocess_config=config["train"]["preprocess"],
        mode="train",
        training=True,
        repeat=True,
    )
    assert data_loader_train is not None  # train data should not be None
    data_loader_val, dataset_val, steps_per_epoch_val = build_dataset(
        dataset_config=config["dataset"],
        preprocess_config=config["train"]["preprocess"],
        mode="valid",
        training=False,
        repeat=True,
    )

    # use strategy to support multiple GPUs
    # the network is mirrored in each GPU so that we can use larger batch size
    # https://www.tensorflow.org/guide/distributed_training
    # only model, optimizer and metrics need to be defined inside the strategy
    num_devices = max(len(tf.config.list_physical_devices("GPU")), 1)
    batch_size = config["train"]["preprocess"]["batch_size"]
    if num_devices > 1:  # pragma: no cover
        strategy = tf.distribute.MirroredStrategy()
        if batch_size % num_devices != 0:
            raise ValueError(
                f"batch size {batch_size} can not be divided evenly "
                f"by the number of devices."
            )
    else:
        strategy = tf.distribute.get_strategy()
    with strategy.scope():
        model: tf.keras.Model = REGISTRY.build_model(
            config=dict(
                name=config["train"]["method"],
                moving_image_size=data_loader_train.moving_image_shape,
                fixed_image_size=data_loader_train.fixed_image_shape,
                index_size=data_loader_train.num_indices,
                labeled=config["dataset"]["labeled"],
                batch_size=batch_size,
                config=config["train"],
            )
        )
        optimizer = opt.build_optimizer(optimizer_config=config["train"]["optimizer"])
        model.compile(optimizer=optimizer)
        model.plot_model(output_dir=log_dir)

    # build callbacks
    tensorboard_callback = tf.keras.callbacks.TensorBoard(
        log_dir=log_dir,
        histogram_freq=config["train"]["save_period"],
        update_freq=config["train"].get("update_freq", "epoch"),
    )
    ckpt_callback, initial_epoch = build_checkpoint_callback(
        model=model,
        dataset=dataset_train,
        log_dir=log_dir,
        save_period=config["train"]["save_period"],
        ckpt_path=ckpt_path,
    )
    callbacks = [tensorboard_callback, ckpt_callback]

    # train
    # it's necessary to define the steps_per_epoch
    # and validation_steps to prevent errors like
    # BaseCollectiveExecutor::StartAbort Out of range: End of sequence
    model.fit(
        x=dataset_train,
        steps_per_epoch=steps_per_epoch_train,
        initial_epoch=initial_epoch,
        epochs=config["train"]["epochs"],
        validation_data=dataset_val,
        validation_steps=steps_per_epoch_val,
        callbacks=callbacks,
    )

    # close file loaders in data loaders after training
    data_loader_train.close()
    if data_loader_val is not None:
        data_loader_val.close()


def main(args=None):
    """
    Entry point for train script.

    :param args: arguments
    """

    parser = argparse.ArgumentParser()

    parser.add_argument(
        "--gpu",
        "-g",
        help="GPU index for training."
        '-g "" for using CPU'
        '-g "0" for using GPU 0'
        '-g "0,1" for using GPU 0 and 1.',
        type=str,
        required=True,
    )

    parser.add_argument(
        "--gpu_allow_growth",
        "-gr",
        help="Prevent TensorFlow from reserving all available GPU memory",
        default=False,
    )

    parser.add_argument(
        "--ckpt_path",
        "-k",
        help="Path of the saved model checkpoint to load."
        "No need to provide if start training from scratch.",
        default="",
        type=str,
        required=False,
    )

    parser.add_argument(
        "--log_dir", help="Path of log directory.", default="logs", type=str
    )

    parser.add_argument(
        "--exp_name",
        "-l",
        help="Name of log directory."
        "The directory is under log root, e.g. logs/ by default."
        "If not provided, a timestamp based folder will be created.",
        default="",
        type=str,
    )

    parser.add_argument(
        "--config_path",
        "-c",
        help="Path of config, must end with .yaml. Can pass multiple paths.",
        type=str,
        nargs="+",
        required=True,
    )

    parser.add_argument(
        "--max_epochs",
        help="The maximum number of epochs, -1 means following configuration.",
        type=int,
        default=-1,
    )

    args = parser.parse_args(args)
    train(
        gpu=args.gpu,
        config_path=args.config_path,
        gpu_allow_growth=args.gpu_allow_growth,
        ckpt_path=args.ckpt_path,
        log_dir=args.log_dir,
        exp_name=args.exp_name,
        max_epochs=args.max_epochs,
    )


if __name__ == "__main__":
    main()  # pragma: no cover


1			# coding=utf-8
2
3			"""
4			Module to train a network using init files and a CLI.
5			"""
6
7			import argparse
8			import os
9			from typing import Dict, List, Tuple, Union
10
11			import tensorflow as tf
12
13			import deepreg.config.parser as config_parser
14			import deepreg.model.optimizer as opt
15			from deepreg.callback import build_checkpoint_callback
16			from deepreg.registry import REGISTRY
17			from deepreg.util import build_dataset, build_log_dir
18
19
20			def build_config(
21			config_path: Union[str, List[str]],
22			log_dir: str,
23			exp_name: str,
24			ckpt_path: str,
25			max_epochs: int = -1,
26			) -> Tuple[Dict, str, str]:
27			"""
28			Function to initialise log directories,
29			assert that checkpointed model is the right
30			type and to parse the configuration for training.
31
32			:param config_path: list of str, path to config file
33			:param log_dir: path of the log directory
34			:param exp_name: name of the experiment
35			:param ckpt_path: path where model is stored.
36			:param max_epochs: if max_epochs > 0, use it to overwrite the configuration
37			:return: - config: a dictionary saving configuration
38			- exp_name: the path of directory to save logs
39			"""
40
41			# init log directory
42			log_dir = build_log_dir(log_dir=log_dir, exp_name=exp_name)
43
44			# load config
45			config = config_parser.load_configs(config_path)
46
47			# replace the ~ with user home path
48			ckpt_path = os.path.expanduser(ckpt_path)
49
50			# overwrite epochs and save_period if necessary
51			if max_epochs > 0:
52			config["train"]["epochs"] = max_epochs
53			config["train"]["save_period"] = min(max_epochs, config["train"]["save_period"])
54
55			# backup config
56			config_parser.save(config=config, out_dir=log_dir)
57
58			return config, log_dir, ckpt_path
59
60
61			def train(
62			gpu: str,
63			config_path: Union[str, List[str]],
64			gpu_allow_growth: bool,
65			ckpt_path: str,
66			exp_name: str = "",
67			log_dir: str = "logs",
68			max_epochs: int = -1,
69			):
70			"""
71			Function to train a model.
72
73			:param gpu: which local gpu to use to train.
74			:param config_path: path to configuration set up.
75			:param gpu_allow_growth: whether to allocate whole GPU memory for training.
76			:param ckpt_path: where to store training checkpoints.
77			:param log_dir: path of the log directory.
78			:param exp_name: experiment name.
79			:param max_epochs: if max_epochs > 0, will use it to overwrite the configuration.
80			"""
81			# set env variables
82			os.environ["CUDA_VISIBLE_DEVICES"] = gpu
83			os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "true" if gpu_allow_growth else "false"
84
85			# load config
86			config, log_dir, ckpt_path = build_config(
87			config_path=config_path,
88			log_dir=log_dir,
89			exp_name=exp_name,
90			ckpt_path=ckpt_path,
91			max_epochs=max_epochs,
92			)
93
94			# build dataset
95			data_loader_train, dataset_train, steps_per_epoch_train = build_dataset(
96			dataset_config=config["dataset"],
97			preprocess_config=config["train"]["preprocess"],
98			mode="train",
99			training=True,
100			repeat=True,
101			)
102			assert data_loader_train is not None # train data should not be None
103			data_loader_val, dataset_val, steps_per_epoch_val = build_dataset(
104			dataset_config=config["dataset"],
105			preprocess_config=config["train"]["preprocess"],
106			mode="valid",
107			training=False,
108			repeat=True,
109			)
110
111			# use strategy to support multiple GPUs
112			# the network is mirrored in each GPU so that we can use larger batch size
113			# https://www.tensorflow.org/guide/distributed_training
114			# only model, optimizer and metrics need to be defined inside the strategy
115			num_devices = max(len(tf.config.list_physical_devices("GPU")), 1)
116			batch_size = config["train"]["preprocess"]["batch_size"]
117			if num_devices > 1: # pragma: no cover
118			strategy = tf.distribute.MirroredStrategy()
119			if batch_size % num_devices != 0:
120			raise ValueError(
121			f"batch size {batch_size} can not be divided evenly "
122			f"by the number of devices."
123			)
124			else:
125			strategy = tf.distribute.get_strategy()
126			with strategy.scope():
127			model: tf.keras.Model = REGISTRY.build_model(
128			config=dict(
129			name=config["train"]["method"],
130			moving_image_size=data_loader_train.moving_image_shape,
131			fixed_image_size=data_loader_train.fixed_image_shape,
132			index_size=data_loader_train.num_indices,
133			labeled=config["dataset"]["labeled"],
134			batch_size=batch_size,
135			config=config["train"],
136			)
137			)
138			optimizer = opt.build_optimizer(optimizer_config=config["train"]["optimizer"])
139			model.compile(optimizer=optimizer)
140			model.plot_model(output_dir=log_dir)
141
142			# build callbacks
143			tensorboard_callback = tf.keras.callbacks.TensorBoard(
144			log_dir=log_dir,
145			histogram_freq=config["train"]["save_period"],
146			update_freq=config["train"].get("update_freq", "epoch"),
147			)
148			ckpt_callback, initial_epoch = build_checkpoint_callback(
149			model=model,
150			dataset=dataset_train,
151			log_dir=log_dir,
152			save_period=config["train"]["save_period"],
153			ckpt_path=ckpt_path,
154			)
155			callbacks = [tensorboard_callback, ckpt_callback]
156
157			# train
158			# it's necessary to define the steps_per_epoch
159			# and validation_steps to prevent errors like
160			# BaseCollectiveExecutor::StartAbort Out of range: End of sequence
161			model.fit(
162			x=dataset_train,
163			steps_per_epoch=steps_per_epoch_train,
164			initial_epoch=initial_epoch,
165			epochs=config["train"]["epochs"],
166			validation_data=dataset_val,
167			validation_steps=steps_per_epoch_val,
168			callbacks=callbacks,
169			)
170
171			# close file loaders in data loaders after training
172			data_loader_train.close()
173			if data_loader_val is not None:
174			data_loader_val.close()
175
176
177			def main(args=None):
178			"""
179			Entry point for train script.
180
181			:param args: arguments
182			"""
183
184			parser = argparse.ArgumentParser()
185
186			parser.add_argument(
187			"--gpu",
188			"-g",
189			help="GPU index for training."
190			'-g "" for using CPU'
191			'-g "0" for using GPU 0'
192			'-g "0,1" for using GPU 0 and 1.',
193			type=str,
194			required=True,
195			)
196
197			parser.add_argument(
198			"--gpu_allow_growth",
199			"-gr",
200			help="Prevent TensorFlow from reserving all available GPU memory",
201			default=False,
202			)
203
204			parser.add_argument(
205			"--ckpt_path",
206			"-k",
207			help="Path of the saved model checkpoint to load."
208			"No need to provide if start training from scratch.",
209			default="",
210			type=str,
211			required=False,
212			)
213
214			parser.add_argument(
215			"--log_dir", help="Path of log directory.", default="logs", type=str
216			)
217
218			parser.add_argument(
219			"--exp_name",
220			"-l",
221			help="Name of log directory."
222			"The directory is under log root, e.g. logs/ by default."
223			"If not provided, a timestamp based folder will be created.",
224			default="",
225			type=str,
226			)
227
228			parser.add_argument(
229			"--config_path",
230			"-c",
231			help="Path of config, must end with .yaml. Can pass multiple paths.",
232			type=str,
233			nargs="+",
234			required=True,
235			)
236
237			parser.add_argument(
238			"--max_epochs",
239			help="The maximum number of epochs, -1 means following configuration.",
240			type=int,
241			default=-1,
242			)
243
244			args = parser.parse_args(args)
245			train(
246			gpu=args.gpu,
247			config_path=args.config_path,
248			gpu_allow_growth=args.gpu_allow_growth,
249			ckpt_path=args.ckpt_path,
250			log_dir=args.log_dir,
251			exp_name=args.exp_name,
252			max_epochs=args.max_epochs,
253			)
254
255
256			if __name__ == "__main__":
257			main() # pragma: no cover
258

DeepRegNet / DeepReg

Pull Request — main (#736)

deepreg.train.main() B

Complexity

Size

Duplication

Importance

How to fix Long Method

Long Method

Duplication Side-by-Side

Filter issues like