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when I run lidc_exp, I found only a single thread is working while loading data
here is my code:
def create_data_gen_pipeline(patient_data, cf, is_training=True): """ create mutli-threaded train/val/test batch generation and augmentation pipeline. :param patient_data: dictionary containing one dictionary per patient in the train/test subset. :param is_training: (optional) whether to perform data augmentation (training) or not (validation/testing) :return: multithreaded_generator """ # create instance of batch generator as first element in pipeline. data_gen = BatchGenerator(patient_data, batch_size=cf.batch_size, cf=cf) # add transformations to pipeline. my_transforms = [] if is_training: mirror_transform = MirrorTransform(axes=np.arange(cf.dim)) my_transforms.append(mirror_transform) spatial_transform = SpatialTransform(patch_size=cf.patch_size[:cf.dim], patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'], do_elastic_deform=cf.da_kwargs['do_elastic_deform'], alpha=cf.da_kwargs['alpha'], sigma=cf.da_kwargs['sigma'], do_rotation=cf.da_kwargs['do_rotation'], angle_x=cf.da_kwargs['angle_x'], angle_y=cf.da_kwargs['angle_y'], angle_z=cf.da_kwargs['angle_z'], do_scale=cf.da_kwargs['do_scale'], scale=cf.da_kwargs['scale'], order_data=cf.da_kwargs['order_data'], random_crop=cf.da_kwargs['random_crop']) my_transforms.append(spatial_transform) else: my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim])) my_transforms.append(ConvertSegToBoundingBoxCoordinates(cf.dim, get_rois_from_seg_flag=False, class_specific_seg_flag=cf.class_specific_seg_flag)) all_transforms = Compose(my_transforms) # multithreaded_generator = SingleThreadedAugmenter(data_gen, all_transforms) if is_training: print (f"is_training: {is_training}, num_processes: {cf.n_workers}") # multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes = cf.n_workers, # num_cached_per_queue=3, seeds=range(cf.n_workers), pin_memory=True) multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes = cf.n_workers, num_cached_per_queue=3, seeds=range(cf.n_workers), pin_memory=True, wait_time=0.01, timeout=5) else: print (f"is_training: {is_training}, num_processes: {max(1, cf.n_workers // 2)}") # multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes = max(1, cf.n_workers // 2), # num_cached_per_queue=1, seeds=None, pin_memory=True) multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes = max(1, cf.n_workers // 2), num_cached_per_queue=1, seeds=None, pin_memory=True, wait_time=0.01, timeout=5) return multithreaded_generator
here is my config:
class configs(DefaultConfigs): def __init__(self, server_env=False): ######################### # Preprocessing # ######################### # self.root_dir = '/home/gregor/networkdrives/E130-Personal/Goetz/Datenkollektive/Lungendaten/Nodules_LIDC_IDRI' # self.raw_data_dir = '{}/new_nrrd'.format(self.root_dir) self.pp_dir = '/root/workspace/medicaldetectiontoolkit/datasets/lidc_mdt' self.target_spacing = (0.7, 0.7, 1.25) ######################### # I/O # ######################### # one out of [2, 3]. dimension the model operates in. self.dim = 3 # one out of ['mrcnn', 'retina_net', 'retina_unet', 'detection_unet', 'ufrcnn']. self.model = 'retina_unet' DefaultConfigs.__init__(self, self.model, server_env, self.dim) ######################### # I/O # ######################### self.test_aug = False self.n_workers = 4
what's wrong? really thanks for your reply
The text was updated successfully, but these errors were encountered:
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when I run lidc_exp, I found only a single thread is working while loading data
here is my code:
here is my config:
what's wrong? really thanks for your reply
The text was updated successfully, but these errors were encountered: