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my_transforms = []
if do_aug:
if cf.da_kwargs["mirror"]:
mirror_transform = Mirror(axes=cf.da_kwargs['mirror_axes'])
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'][:2],
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'],
random_crop=cf.da_kwargs['random_crop'],
border_mode_data=cf.da_kwargs['border_mode_data'])
my_transforms.append(spatial_transform)
gamma_transform = GammaTransform(gamma_range=cf.da_kwargs["gamma_range"], invert_image=False,
per_channel=False, retain_stats=False)
my_transforms.append(gamma_transform)
else:
my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim]))
if cf.create_bounding_box_targets:
my_transforms.append(ConvertSegToBoundingBoxCoordinates(cf.dim, cf.roi_items, False, cf.class_specific_seg))
#batch receives entry 'bb_target' w bbox coordinates as [y1,x1,y2,x2,z1,z2].
#my_transforms.append(ConvertSegToOnehotTransform(classes=range(cf.num_seg_classes)))
all_transforms = Compose(my_transforms)
#MTAugmenter creates iterator from data iterator data_gen after applying the composed transform all_transforms
multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes=cf.n_workers,
seeds=np.random.randint(0,cf.n_workers*2,size=cf.n_workers))
return multithreaded_generator
"""
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 test_pids: (optional) list of test patient ids, calls the test generator.
:param do_aug: (optional) whether to perform data augmentation (training) or not (validation/testing)
:return: multithreaded_generator
"""
data_gen = BatchGenerator(cf, patient_data, sample_pids_w_replace=sample_pids_w_replace)
my_transforms = []
if do_aug:
if cf.da_kwargs["mirror"]:
mirror_transform = Mirror(axes=cf.da_kwargs['mirror_axes'])
my_transforms.append(mirror_transform)
if cf.da_kwargs["gamma_transform"]:
gamma_transform = GammaTransform(gamma_range=cf.da_kwargs["gamma_range"], invert_image=False,
per_channel=False, retain_stats=True)
my_transforms.append(gamma_transform)
if cf.dim == 3:
# augmentations with desired effect on z-dimension
spatial_transform = SpatialTransform(patch_size=cf.patch_size,
patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'],
do_elastic_deform=False,
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'],
random_crop=cf.da_kwargs['random_crop'],
border_mode_data=cf.da_kwargs['border_mode_data'])
my_transforms.append(spatial_transform)
# augmentations that are only meant to affect x-y
my_transforms.append(Convert3DTo2DTransform())
spatial_transform = SpatialTransform(patch_size=cf.patch_size[:2],