import argparse import gc import itertools import math import os import sys from pathlib import Path from typing import Union, List, Any import cv2 import numpy as np os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' stderr = sys.stderr sys.stderr = open(os.devnull, 'w') import tensorflow as tf from tensorflow.python.keras.saving.save import load_model sys.stderr = stderr from mpire import WorkerPool from mpire.utils import make_single_arguments class SbbBinarizer: def __init__(self) -> None: super().__init__() self.model: Any = None self.model_height: int = 0 self.model_width: int = 0 self.n_classes: int = 0 def load_model(self, model_dir: Union[str, Path]): model_dir = Path(model_dir) self.model = load_model(str(model_dir.absolute()), compile=False) self.model_height = self.model.layers[len(self.model.layers) - 1].output_shape[1] self.model_width = self.model.layers[len(self.model.layers) - 1].output_shape[2] self.n_classes = self.model.layers[len(self.model.layers) - 1].output_shape[3] def binarize_image(self, image_path: Path, save_path: Path): if not image_path.exists(): raise ValueError(f"Image not found: {str(image_path)}") # noinspection PyUnresolvedReferences img = cv2.imread(str(image_path)) original_image_height, original_image_width, image_channels = img.shape # Padded images must be multiples of model size padded_image_height = math.ceil(original_image_height / self.model_height) * self.model_height padded_image_width = math.ceil(original_image_width / self.model_width) * self.model_width padded_image = np.zeros((padded_image_height, padded_image_width, image_channels)) padded_image[0:original_image_height, 0:original_image_width, :] = img[:, :, :] image_batch = np.expand_dims(padded_image, 0) # Create the batch dimension patches = tf.image.extract_patches( images=image_batch, sizes=[1, self.model_height, self.model_width, 1], strides=[1, self.model_height, self.model_width, 1], rates=[1, 1, 1, 1], padding='SAME' ) number_of_horizontal_patches = patches.shape[1] number_of_vertical_patches = patches.shape[2] total_number_of_patches = number_of_horizontal_patches * number_of_vertical_patches target_shape = (total_number_of_patches, self.model_height, self.model_width, image_channels) # Squeeze all image patches (n, m, width, height, channels) into a single big batch (b, width, height, channels) image_patches = tf.reshape(patches, target_shape) # Normalize the image to values between 0.0 - 1.0 image_patches = image_patches / float(255.0) predicted_patches = self.model.predict(image_patches) # We have to manually call garbage collection and clear_session here to avoid memory leaks. # Taken from https://medium.com/dive-into-ml-ai/dealing-with-memory-leak-issue-in-keras-model-training-e703907a6501 gc.collect() tf.keras.backend.clear_session() # The result is a white-on-black image that needs to be inverted to be displayed as black-on-white image # We do this by converting the binary values to a boolean numpy-array and then inverting the values black_on_white_patches = np.invert(np.argmax(predicted_patches, axis=3).astype(bool)) # cv2 can't export a boolean numpy array into a black-and-white PNG image, so we have to convert it to uint8 (grayscale) values grayscale_patches = black_on_white_patches.astype(np.uint8) * 255 full_image_with_padding = self._patches_to_image( grayscale_patches, padded_image_height, padded_image_width, self.model_height, self.model_width ) full_image = full_image_with_padding[0:original_image_height, 0:original_image_width] Path(save_path).parent.mkdir(parents=True, exist_ok=True) # noinspection PyUnresolvedReferences cv2.imwrite(str(save_path), full_image) def _patches_to_image(self, patches: np.ndarray, image_height: int, image_width: int, patch_height: int, patch_width: int): height = math.ceil(image_height / patch_height) * patch_height width = math.ceil(image_width / patch_width) * patch_width image_reshaped = np.reshape( np.squeeze(patches), [height // patch_height, width // patch_width, patch_height, patch_width] ) image_transposed = np.transpose(a=image_reshaped, axes=[0, 2, 1, 3]) image_resized = np.reshape(image_transposed, [height, width]) return image_resized def split_list_into_worker_batches(files: List[Any], number_of_workers: int) -> List[List[Any]]: """ Splits any given list into batches for the specified number of workers and returns a list of lists. """ batches = [] batch_size = math.ceil(len(files) / number_of_workers) batch_start = 0 for i in range(1, number_of_workers + 1): batch_end = i * batch_size file_batch_to_delete = files[batch_start: batch_end] batches.append(file_batch_to_delete) batch_start = batch_end return batches def batch_predict(input_data): model_dir, input_images, output_images, worker_number = input_data print(f"Setting visible cuda devices to {str(worker_number)}") # Each worker thread will be assigned only one of the available GPUs to allow multiprocessing across GPUs os.environ["CUDA_VISIBLE_DEVICES"] = str(worker_number) binarizer = SbbBinarizer() binarizer.load_model(model_dir) for image_path, output_path in zip(input_images, output_images): binarizer.binarize_image(image_path=image_path, save_path=output_path) print(f"Binarized {image_path}") if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('-m', '--model_dir', default="model_2021_03_09", help="Path to the directory where the TF model resides or path to an h5 file.") parser.add_argument('-i', '--input-path', required=True) parser.add_argument('-o', '--output-path', required=True) args = parser.parse_args() input_path = Path(args.input_path) output_path = Path(args.output_path) model_directory = args.model_dir if input_path.is_dir(): print(f"Enumerating all PNG files in {str(input_path)}") all_input_images = list(input_path.rglob("*.png")) print(f"Filtering images that have already been binarized in {str(output_path)}") input_images = [i for i in all_input_images if not (output_path / (i.relative_to(input_path))).exists()] output_images = [output_path / (i.relative_to(input_path)) for i in input_images] input_images = [i for i in input_images] print(f"Starting batch-binarization of {len(input_images)} images") number_of_gpus = len(tf.config.list_physical_devices('GPU')) number_of_workers = max(1, number_of_gpus) image_batches = split_list_into_worker_batches(input_images, number_of_workers) output_batches = split_list_into_worker_batches(output_images, number_of_workers) # Must use spawn to create completely new process that has its own resources to properly multiprocess across GPUs with WorkerPool(n_jobs=number_of_workers, start_method='spawn') as pool: model_dirs = itertools.repeat(model_directory, len(image_batches)) input_data = zip(model_dirs, image_batches, output_batches, range(number_of_workers)) contents = pool.map_unordered( batch_predict, make_single_arguments(input_data), iterable_len=number_of_workers, progress_bar=False ) else: binarizer = SbbBinarizer() binarizer.load_model(model_directory) binarizer.binarize_image(image_path=input_path, save_path=output_path)