deepreg.predict.predict() - Code Metrics - Inspection of "Merge pull request #724 from DeepRegNet/720-add-op..." - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

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by Yunguan

created 2021-04-16 22:17 UTC

deepreg.predict.predict() C

↳ Parent: deepreg.predict

Complexity

Conditions

Size

Total Lines	125
Code Lines	70

Duplication

Lines	13
Ratio	10.4 %

Importance

Changes

Metric	Value
eloc	70
dl	13
loc	125
rs	6.5818
c	0
b	0
f	0
cc	7
nop	11

How to fix Long Method Many Parameters

# coding=utf-8

"""
Module to perform predictions on data using
command line interface.
"""

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

import numpy as np
import tensorflow as tf

import deepreg.config.parser as config_parser
import deepreg.model.layer_util as layer_util
import deepreg.model.optimizer as opt
from deepreg import log
from deepreg.callback import build_checkpoint_callback
from deepreg.registry import REGISTRY
from deepreg.util import (
    build_dataset,
    build_log_dir,
    calculate_metrics,
    save_array,
    save_metric_dict,
)

logger = log.get(__name__)


def build_pair_output_path(indices: list, save_dir: str) -> Tuple[str, str]:
    """
    Create directory for saving the paired data

    :param indices: indices of the pair, the last one is for label
    :param save_dir: directory of output
    :return: - save_dir, str, directory for saving the moving/fixed image
             - label_dir, str, directory for saving the rest outputs
    """

    # cast indices to string and init directory name
    pair_index = "pair_" + "_".join([str(x) for x in indices[:-1]])
    pair_dir = os.path.join(save_dir, pair_index)
    os.makedirs(pair_dir, exist_ok=True)

    if indices[-1] >= 0:
        label_index = f"label_{indices[-1]}"
        label_dir = os.path.join(pair_dir, label_index)
        os.makedirs(label_dir, exist_ok=True)
    else:
        label_dir = pair_dir

    return pair_dir, label_dir


def predict_on_dataset(
    dataset: tf.data.Dataset,
    fixed_grid_ref: tf.Tensor,
    model: tf.keras.Model,
    model_method: str,
    save_dir: str,
    save_nifti: bool,
    save_png: bool,
):
    """
    Function to predict results from a dataset from some model

    :param dataset: where data is stored
    :param fixed_grid_ref: shape=(1, f_dim1, f_dim2, f_dim3, 3)
    :param model: model to be used for prediction
    :param model_method: ddf / dvf / affine / conditional
    :param save_dir: path to store dir
    :param save_nifti: if true, outputs will be saved in nifti format
    :param save_png: if true, outputs will be saved in png format
    """
    # remove the save_dir in case it exists
    if os.path.exists(save_dir):
        shutil.rmtree(save_dir)  # pragma: no cover

    sample_index_strs = []
    metric_lists = []
    for _, inputs in enumerate(dataset):
        batch_size = inputs[list(inputs.keys())[0]].shape[0]
        outputs = model.predict(x=inputs, batch_size=batch_size)
        indices, processed = model.postprocess(inputs=inputs, outputs=outputs)

        # convert to np arrays
        indices = indices.numpy()
        processed = {
            k: (v[0].numpy() if isinstance(v[0], tf.Tensor) else v[0], v[1], v[2])
            for k, v in processed.items()
        }

        # save images of inputs and outputs
        for sample_index in range(batch_size):
            # save label independent tensors under pair_dir, otherwise under label_dir

            # init output path
            indices_i = indices[sample_index, :].astype(int).tolist()
            pair_dir, label_dir = build_pair_output_path(
                indices=indices_i, save_dir=save_dir
            )

            for name, (arr, normalize, on_label) in processed.items():
                if name == "theta":
                    np.savetxt(
                        fname=os.path.join(pair_dir, "affine.txt"),
                        X=arr[sample_index, :, :],
                        delimiter=",",
                    )
                    continue

                arr_save_dir = label_dir if on_label else pair_dir
                save_array(
                    save_dir=arr_save_dir,
                    arr=arr[sample_index, :, :, :],
                    name=name,
                    normalize=normalize,  # label's value is already in [0, 1]
                    save_nifti=save_nifti,
                    save_png=save_png,
                    overwrite=arr_save_dir == label_dir,
                )

            # calculate metric
            sample_index_str = "_".join([str(x) for x in indices_i])
            if sample_index_str in sample_index_strs:  # pragma: no cover
                raise ValueError(
                    "Sample is repeated, maybe the dataset has been repeated."
                )
            sample_index_strs.append(sample_index_str)

            metric = calculate_metrics(
                fixed_image=processed["fixed_image"][0],
                fixed_label=processed["fixed_label"][0] if model.labeled else None,
                pred_fixed_image=processed["pred_fixed_image"][0],
                pred_fixed_label=processed["pred_fixed_label"][0]
                if model.labeled
                else None,
                fixed_grid_ref=fixed_grid_ref,
                sample_index=sample_index,
            )
            metric["pair_index"] = indices_i[:-1]
            metric["label_index"] = indices_i[-1]
            metric_lists.append(metric)

    # save metric
    save_metric_dict(save_dir=save_dir, metrics=metric_lists)


def build_config(
    config_path: Union[str, List[str]], log_dir: str, exp_name: str, ckpt_path: str
) -> Tuple[Dict, str, str]:
    """
    Function to create new directory to log directory to store results.

    :param config_path: path of configuration files.
    :param log_dir: path of the log directory.
    :param exp_name: experiment name.
    :param ckpt_path: path where model is stored.
    :return: - config, configuration dictionary.
             - exp_name, path of the directory for saving outputs.
    """

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

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

    # load config
    if config_path == "":
        # use default config, which should be provided in the log folder
        config = config_parser.load_configs(
            "/".join(ckpt_path.split("/")[:-2]) + "/config.yaml"
        )
    else:
        # use customized config
        logger.warning(
            "Using customized configuration. "
            "The code might break if the config doesn't match the saved model."
        )
        config = config_parser.load_configs(config_path)
    return config, log_dir, ckpt_path


def predict(
    gpu: str,
    ckpt_path: str,
    mode: str,
    batch_size: int,
    exp_name: str,
    config_path: Union[str, List[str]],
    num_workers: int = 1,
    gpu_allow_growth: bool = True,
    save_nifti: bool = True,
    save_png: bool = True,
    log_dir: str = "logs",
):
    """
    Function to predict some metrics from the saved model and logging results.

    :param gpu: which env gpu to use.
    :param ckpt_path: where model is stored, should be like log_folder/save/ckpt-x.
    :param mode: train / valid / test, to define which split of dataset to be evaluated.
    :param batch_size: int, batch size to perform predictions.
    :param exp_name: name of the experiment.
    :param config_path: to overwrite the default config.
    :param num_workers: number of cpu cores to be used, <=0 means not limited.
    :param gpu_allow_growth: whether to allocate whole GPU memory for training.
    :param save_nifti: if true, outputs will be saved in nifti format.
    :param save_png: if true, outputs will be saved in png format.
    :param log_dir: path of the log directory.
    """

    # env vars
    os.environ["CUDA_VISIBLE_DEVICES"] = gpu
    os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "false" if gpu_allow_growth else "true"
    if num_workers <= 0:  # pragma: no cover

        logger.info(
            "Limiting CPU usage by setting environment variables "
            "OMP_NUM_THREADS, TF_NUM_INTRAOP_THREADS, TF_NUM_INTEROP_THREADS to %d. "
            "This may slow down the prediction. "
            "Please use --num_workers flag to modify the behavior. "
            "Setting to 0 or negative values will remove the limitation.",
            num_workers,
        )
        # limit CPU usage
        # https://github.com/tensorflow/tensorflow/issues/29968#issuecomment-789604232
        os.environ["OMP_NUM_THREADS"] = str(num_workers)
        os.environ["TF_NUM_INTRAOP_THREADS"] = str(num_workers)
        os.environ["TF_NUM_INTEROP_THREADS"] = str(num_workers)

    # 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
    )
    config["train"]["preprocess"]["batch_size"] = batch_size

    # data
    data_loader, dataset, _ = build_dataset(
        dataset_config=config["dataset"],
        preprocess_config=config["train"]["preprocess"],
        mode=mode,
        training=False,
        repeat=False,
    )
    assert data_loader is not None

    # 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)
    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.moving_image_shape,
                fixed_image_size=data_loader.fixed_image_shape,
                index_size=data_loader.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)

    # load weights
    if ckpt_path.endswith(".ckpt"):
        # for ckpt from tf.keras.callbacks.ModelCheckpoint
        # skip warnings because of optimizers
        # https://stackoverflow.com/questions/58289342/tf2-0-translation-model-error-when-restoring-the-saved-model-unresolved-object
        model.load_weights(ckpt_path).expect_partial()  # pragma: no cover
    else:
        # for ckpts from ckpt manager callback
        _, _ = build_checkpoint_callback(
            model=model,
            dataset=dataset,
            log_dir=log_dir,
            save_period=config["train"]["save_period"],
            ckpt_path=ckpt_path,
        )

    # predict
    fixed_grid_ref = tf.expand_dims(
        layer_util.get_reference_grid(grid_size=data_loader.fixed_image_shape), axis=0
    )  # shape = (1, f_dim1, f_dim2, f_dim3, 3)
    predict_on_dataset(
        dataset=dataset,
        fixed_grid_ref=fixed_grid_ref,
        model=model,
        model_method=config["train"]["method"],
        save_dir=os.path.join(log_dir, "test"),
        save_nifti=save_nifti,
        save_png=save_png,
    )

    # close the opened files in data loaders
    data_loader.close()


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

    :param args:
    """
    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(
        "--num_workers",
        help="Number of CPUs to be used, <= 0 means unlimited.",
        type=int,
        default=1,
    )

    parser.add_argument(
        "--ckpt_path",
        "-k",
        help="Path of checkpointed model to load",
        default="",
        type=str,
        required=True,
    )

    parser.add_argument(
        "--mode",
        "-m",
        help="Define the split of data to be used for prediction."
        "train or valid or test",
        type=str,
        default="test",
        required=True,
    )

    parser.add_argument(
        "--batch_size", "-b", help="Batch size for predictions", default=1, type=int
    )

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

    parser.add_argument(
        "--exp_name", "-n", help="Name of the experiment.", default="", type=str
    )

    parser.add_argument("--save_nifti", dest="nifti", action="store_true")
    parser.add_argument("--no_nifti", dest="nifti", action="store_false")
    parser.set_defaults(nifti=True)

    parser.add_argument("--save_png", dest="png", action="store_true")
    parser.add_argument("--no_png", dest="png", action="store_false")
    parser.set_defaults(png=False)

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

    args = parser.parse_args(args)

    predict(
        gpu=args.gpu,
        ckpt_path=args.ckpt_path,
        num_workers=args.num_workers,
        gpu_allow_growth=args.gpu_allow_growth,
        mode=args.mode,
        batch_size=args.batch_size,
        log_dir=args.log_dir,
        exp_name=args.exp_name,
        config_path=args.config_path,
        save_nifti=args.nifti,
        save_png=args.png,
    )


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


1		# coding=utf-8
2
3		"""
4		Module to perform predictions on data using
5		command line interface.
6		"""
7
8		import argparse
9		import os
10		import shutil
11		from typing import Dict, List, Tuple, Union
12
13		import numpy as np
14		import tensorflow as tf
15
16		import deepreg.config.parser as config_parser
17		import deepreg.model.layer_util as layer_util
18		import deepreg.model.optimizer as opt
19		from deepreg import log
20		from deepreg.callback import build_checkpoint_callback
21		from deepreg.registry import REGISTRY
22		from deepreg.util import (
23		build_dataset,
24		build_log_dir,
25		calculate_metrics,
26		save_array,
27		save_metric_dict,
28		)
29
30		logger = log.get(__name__)
31
32
33		def build_pair_output_path(indices: list, save_dir: str) -> Tuple[str, str]:
34		"""
35		Create directory for saving the paired data
36
37		:param indices: indices of the pair, the last one is for label
38		:param save_dir: directory of output
39		:return: - save_dir, str, directory for saving the moving/fixed image
40		- label_dir, str, directory for saving the rest outputs
41		"""
42
43		# cast indices to string and init directory name
44		pair_index = "pair_" + "_".join([str(x) for x in indices[:-1]])
45		pair_dir = os.path.join(save_dir, pair_index)
46		os.makedirs(pair_dir, exist_ok=True)
47
48		if indices[-1] >= 0:
49		label_index = f"label_{indices[-1]}"
50		label_dir = os.path.join(pair_dir, label_index)
51		os.makedirs(label_dir, exist_ok=True)
52		else:
53		label_dir = pair_dir
54
55		return pair_dir, label_dir
56
57
58		def predict_on_dataset(
59		dataset: tf.data.Dataset,
60		fixed_grid_ref: tf.Tensor,
61		model: tf.keras.Model,
62		model_method: str,
63		save_dir: str,
64		save_nifti: bool,
65		save_png: bool,
66		):
67		"""
68		Function to predict results from a dataset from some model
69
70		:param dataset: where data is stored
71		:param fixed_grid_ref: shape=(1, f_dim1, f_dim2, f_dim3, 3)
72		:param model: model to be used for prediction
73		:param model_method: ddf / dvf / affine / conditional
74		:param save_dir: path to store dir
75		:param save_nifti: if true, outputs will be saved in nifti format
76		:param save_png: if true, outputs will be saved in png format
77		"""
78		# remove the save_dir in case it exists
79		if os.path.exists(save_dir):
80		shutil.rmtree(save_dir) # pragma: no cover
81
82		sample_index_strs = []
83		metric_lists = []
84		for _, inputs in enumerate(dataset):
85		batch_size = inputs[list(inputs.keys())[0]].shape[0]
86		outputs = model.predict(x=inputs, batch_size=batch_size)
87		indices, processed = model.postprocess(inputs=inputs, outputs=outputs)
88
89		# convert to np arrays
90		indices = indices.numpy()
91		processed = {
92		k: (v[0].numpy() if isinstance(v[0], tf.Tensor) else v[0], v[1], v[2])
93		for k, v in processed.items()
94		}
95
96		# save images of inputs and outputs
97		for sample_index in range(batch_size):
98		# save label independent tensors under pair_dir, otherwise under label_dir
99
100		# init output path
101		indices_i = indices[sample_index, :].astype(int).tolist()
102		pair_dir, label_dir = build_pair_output_path(
103		indices=indices_i, save_dir=save_dir
104		)
105
106		for name, (arr, normalize, on_label) in processed.items():
107		if name == "theta":
108		np.savetxt(
109		fname=os.path.join(pair_dir, "affine.txt"),
110		X=arr[sample_index, :, :],
111		delimiter=",",
112		)
113		continue
114
115		arr_save_dir = label_dir if on_label else pair_dir
116		save_array(
117		save_dir=arr_save_dir,
118		arr=arr[sample_index, :, :, :],
119		name=name,
120		normalize=normalize, # label's value is already in [0, 1]
121		save_nifti=save_nifti,
122		save_png=save_png,
123		overwrite=arr_save_dir == label_dir,
124		)
125
126		# calculate metric
127		sample_index_str = "_".join([str(x) for x in indices_i])
128		if sample_index_str in sample_index_strs: # pragma: no cover
129		raise ValueError(
130		"Sample is repeated, maybe the dataset has been repeated."
131		)
132		sample_index_strs.append(sample_index_str)
133
134		metric = calculate_metrics(
135		fixed_image=processed["fixed_image"][0],
136		fixed_label=processed["fixed_label"][0] if model.labeled else None,
137		pred_fixed_image=processed["pred_fixed_image"][0],
138		pred_fixed_label=processed["pred_fixed_label"][0]
139		if model.labeled
140		else None,
141		fixed_grid_ref=fixed_grid_ref,
142		sample_index=sample_index,
143		)
144		metric["pair_index"] = indices_i[:-1]
145		metric["label_index"] = indices_i[-1]
146		metric_lists.append(metric)
147
148		# save metric
149		save_metric_dict(save_dir=save_dir, metrics=metric_lists)
150
151
152		def build_config(
153		config_path: Union[str, List[str]], log_dir: str, exp_name: str, ckpt_path: str
154		) -> Tuple[Dict, str, str]:
155		"""
156		Function to create new directory to log directory to store results.
157
158		:param config_path: path of configuration files.
159		:param log_dir: path of the log directory.
160		:param exp_name: experiment name.
161		:param ckpt_path: path where model is stored.
162		:return: - config, configuration dictionary.
163		- exp_name, path of the directory for saving outputs.
164		"""
165
166		# init log directory
167		log_dir = build_log_dir(log_dir=log_dir, exp_name=exp_name)
168
169		# replace the ~ with user home path
170		ckpt_path = os.path.expanduser(ckpt_path)
171
172		# load config
173		if config_path == "":
174		# use default config, which should be provided in the log folder
175		config = config_parser.load_configs(
176		"/".join(ckpt_path.split("/")[:-2]) + "/config.yaml"
177		)
178		else:
179		# use customized config
180		logger.warning(
181		"Using customized configuration. "
182		"The code might break if the config doesn't match the saved model."
183		)
184		config = config_parser.load_configs(config_path)
185		return config, log_dir, ckpt_path
186
187
188		def predict(
189		gpu: str,
190		ckpt_path: str,
191		mode: str,
192		batch_size: int,
193		exp_name: str,
194		config_path: Union[str, List[str]],
195		num_workers: int = 1,
196		gpu_allow_growth: bool = True,
197		save_nifti: bool = True,
198		save_png: bool = True,
199		log_dir: str = "logs",
200		):
201		"""
202		Function to predict some metrics from the saved model and logging results.
203
204		:param gpu: which env gpu to use.
205		:param ckpt_path: where model is stored, should be like log_folder/save/ckpt-x.
206		:param mode: train / valid / test, to define which split of dataset to be evaluated.
207		:param batch_size: int, batch size to perform predictions.
208		:param exp_name: name of the experiment.
209		:param config_path: to overwrite the default config.
210		:param num_workers: number of cpu cores to be used, <=0 means not limited.
211		:param gpu_allow_growth: whether to allocate whole GPU memory for training.
212		:param save_nifti: if true, outputs will be saved in nifti format.
213		:param save_png: if true, outputs will be saved in png format.
214		:param log_dir: path of the log directory.
215		"""
216
217		# env vars
218		os.environ["CUDA_VISIBLE_DEVICES"] = gpu
219		os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "false" if gpu_allow_growth else "true"
220	View Code Duplication	if num_workers <= 0: # pragma: no cover
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221		logger.info(
222		"Limiting CPU usage by setting environment variables "
223		"OMP_NUM_THREADS, TF_NUM_INTRAOP_THREADS, TF_NUM_INTEROP_THREADS to %d. "
224		"This may slow down the prediction. "
225		"Please use --num_workers flag to modify the behavior. "
226		"Setting to 0 or negative values will remove the limitation.",
227		num_workers,
228		)
229		# limit CPU usage
230		# https://github.com/tensorflow/tensorflow/issues/29968#issuecomment-789604232
231		os.environ["OMP_NUM_THREADS"] = str(num_workers)
232		os.environ["TF_NUM_INTRAOP_THREADS"] = str(num_workers)
233		os.environ["TF_NUM_INTEROP_THREADS"] = str(num_workers)
234
235		# load config
236		config, log_dir, ckpt_path = build_config(
237		config_path=config_path, log_dir=log_dir, exp_name=exp_name, ckpt_path=ckpt_path
238		)
239		config["train"]["preprocess"]["batch_size"] = batch_size
240
241		# data
242		data_loader, dataset, _ = build_dataset(
243		dataset_config=config["dataset"],
244		preprocess_config=config["train"]["preprocess"],
245		mode=mode,
246		training=False,
247		repeat=False,
248		)
249		assert data_loader is not None
250
251		# use strategy to support multiple GPUs
252		# the network is mirrored in each GPU so that we can use larger batch size
253		# https://www.tensorflow.org/guide/distributed_training
254		# only model, optimizer and metrics need to be defined inside the strategy
255		num_devices = max(len(tf.config.list_physical_devices("GPU")), 1)
256		if num_devices > 1: # pragma: no cover
257		strategy = tf.distribute.MirroredStrategy()
258		if batch_size % num_devices != 0:
259		raise ValueError(
260		f"batch size {batch_size} can not be divided evenly "
261		f"by the number of devices."
262		)
263		else:
264		strategy = tf.distribute.get_strategy()
265		with strategy.scope():
266		model: tf.keras.Model = REGISTRY.build_model(
267		config=dict(
268		name=config["train"]["method"],
269		moving_image_size=data_loader.moving_image_shape,
270		fixed_image_size=data_loader.fixed_image_shape,
271		index_size=data_loader.num_indices,
272		labeled=config["dataset"]["labeled"],
273		batch_size=batch_size,
274		config=config["train"],
275		)
276		)
277		optimizer = opt.build_optimizer(optimizer_config=config["train"]["optimizer"])
278		model.compile(optimizer=optimizer)
279		model.plot_model(output_dir=log_dir)
280
281		# load weights
282		if ckpt_path.endswith(".ckpt"):
283		# for ckpt from tf.keras.callbacks.ModelCheckpoint
284		# skip warnings because of optimizers
285		# https://stackoverflow.com/questions/58289342/tf2-0-translation-model-error-when-restoring-the-saved-model-unresolved-object
286		model.load_weights(ckpt_path).expect_partial() # pragma: no cover
287		else:
288		# for ckpts from ckpt manager callback
289		_, _ = build_checkpoint_callback(
290		model=model,
291		dataset=dataset,
292		log_dir=log_dir,
293		save_period=config["train"]["save_period"],
294		ckpt_path=ckpt_path,
295		)
296
297		# predict
298		fixed_grid_ref = tf.expand_dims(
299		layer_util.get_reference_grid(grid_size=data_loader.fixed_image_shape), axis=0
300		) # shape = (1, f_dim1, f_dim2, f_dim3, 3)
301		predict_on_dataset(
302		dataset=dataset,
303		fixed_grid_ref=fixed_grid_ref,
304		model=model,
305		model_method=config["train"]["method"],
306		save_dir=os.path.join(log_dir, "test"),
307		save_nifti=save_nifti,
308		save_png=save_png,
309		)
310
311		# close the opened files in data loaders
312		data_loader.close()
313
314
315		def main(args=None):
316		"""
317		Entry point for predict script.
318
319		:param args:
320		"""
321		parser = argparse.ArgumentParser()
322
323		parser.add_argument(
324		"--gpu",
325		"-g",
326		help="GPU index for training."
327		'-g "" for using CPU'
328		'-g "0" for using GPU 0'
329		'-g "0,1" for using GPU 0 and 1.',
330		type=str,
331		required=True,
332		)
333
334		parser.add_argument(
335		"--gpu_allow_growth",
336		"-gr",
337		help="Prevent TensorFlow from reserving all available GPU memory",
338		default=False,
339		)
340
341		parser.add_argument(
342		"--num_workers",
343		help="Number of CPUs to be used, <= 0 means unlimited.",
344		type=int,
345		default=1,
346		)
347
348		parser.add_argument(
349		"--ckpt_path",
350		"-k",
351		help="Path of checkpointed model to load",
352		default="",
353		type=str,
354		required=True,
355		)
356
357		parser.add_argument(
358		"--mode",
359		"-m",
360		help="Define the split of data to be used for prediction."
361		"train or valid or test",
362		type=str,
363		default="test",
364		required=True,
365		)
366
367		parser.add_argument(
368		"--batch_size", "-b", help="Batch size for predictions", default=1, type=int
369		)
370
371		parser.add_argument(
372		"--log_dir", help="Path of log directory.", default="logs", type=str
373		)
374
375		parser.add_argument(
376		"--exp_name", "-n", help="Name of the experiment.", default="", type=str
377		)
378
379		parser.add_argument("--save_nifti", dest="nifti", action="store_true")
380		parser.add_argument("--no_nifti", dest="nifti", action="store_false")
381		parser.set_defaults(nifti=True)
382
383		parser.add_argument("--save_png", dest="png", action="store_true")
384		parser.add_argument("--no_png", dest="png", action="store_false")
385		parser.set_defaults(png=False)
386
387		parser.add_argument(
388		"--config_path",
389		"-c",
390		help="Path of config, must end with .yaml. Can pass multiple paths.",
391		type=str,
392		nargs="*",
393		default="",
394		)
395
396		args = parser.parse_args(args)
397
398		predict(
399		gpu=args.gpu,
400		ckpt_path=args.ckpt_path,
401		num_workers=args.num_workers,
402		gpu_allow_growth=args.gpu_allow_growth,
403		mode=args.mode,
404		batch_size=args.batch_size,
405		log_dir=args.log_dir,
406		exp_name=args.exp_name,
407		config_path=args.config_path,
408		save_nifti=args.nifti,
409		save_png=args.png,
410		)
411
412
413		if __name__ == "__main__":
414		main() # pragma: no cover
415

DeepRegNet / DeepReg

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deepreg.predict.predict() C

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