default_config.py

# Implementation of this model is borrowed and modified
# (from torch to paddle) from here:
# https://github.com/MIC-DKFZ/nnUNet

# Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from copy import deepcopy

default_3D_augmentation_params = {
    "selected_data_channels": None,
    "selected_seg_channels": None,
    "do_elastic": True,
    "elastic_deform_alpha": (0., 900.),
    "elastic_deform_sigma": (9., 13.),
    "p_eldef": 0.2,
    "do_scaling": True,
    "scale_range": (0.85, 1.25),
    "independent_scale_factor_for_each_axis": False,
    "p_independent_scale_per_axis": 1,
    "p_scale": 0.2,
    "do_rotation": True,
    "rotation_x": (-15. / 360 * 2. * np.pi, 15. / 360 * 2. * np.pi),
    "rotation_y": (-15. / 360 * 2. * np.pi, 15. / 360 * 2. * np.pi),
    "rotation_z": (-15. / 360 * 2. * np.pi, 15. / 360 * 2. * np.pi),
    "rotation_p_per_axis": 1,
    "p_rot": 0.2,
    "random_crop": False,
    "random_crop_dist_to_border": None,
    "do_gamma": True,
    "gamma_retain_stats": True,
    "gamma_range": (0.7, 1.5),
    "p_gamma": 0.3,
    "do_mirror": True,
    "mirror_axes": (0, 1, 2),
    "dummy_2D": False,
    "mask_was_used_for_normalization": None,
    "border_mode_data": "constant",
    "all_segmentation_labels": None,
    "move_last_seg_chanel_to_data": False,
    "cascade_do_cascade_augmentations": False,
    "cascade_random_binary_transform_p": 0.4,
    "cascade_random_binary_transform_p_per_label": 1,
    "cascade_random_binary_transform_size": (1, 8),
    "cascade_remove_conn_comp_p": 0.2,
    "cascade_remove_conn_comp_max_size_percent_threshold": 0.15,
    "cascade_remove_conn_comp_fill_with_other_class_p": 0.0,
    "do_additive_brightness": False,
    "additive_brightness_p_per_sample": 0.15,
    "additive_brightness_p_per_channel": 0.5,
    "additive_brightness_mu": 0.0,
    "additive_brightness_sigma": 0.1,
    "num_threads": 8,
    "num_cached_per_thread": 1,
}

default_2D_augmentation_params = deepcopy(default_3D_augmentation_params)

default_2D_augmentation_params["elastic_deform_alpha"] = (0., 200.)
default_2D_augmentation_params["elastic_deform_sigma"] = (9., 13.)
default_2D_augmentation_params["rotation_x"] = (-180. / 360 * 2. * np.pi,
                                                180. / 360 * 2. * np.pi)
default_2D_augmentation_params["rotation_y"] = (-0. / 360 * 2. * np.pi,
                                                0. / 360 * 2. * np.pi)
default_2D_augmentation_params["rotation_z"] = (-0. / 360 * 2. * np.pi,
                                                0. / 360 * 2. * np.pi)

default_2D_augmentation_params["dummy_2D"] = False
default_2D_augmentation_params["mirror_axes"] = (0, 1)