# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany # # 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. from copy import deepcopy from nnunet.experiment_planning.common_utils import get_pool_and_conv_props from nnunet.experiment_planning.experiment_planner_baseline_2DUNet import ExperimentPlanner2D from nnunet.network_architecture.generic_UNet import Generic_UNet from nnunet.paths import * import numpy as np class ExperimentPlanner2D_v21(ExperimentPlanner2D): def __init__(self, folder_with_cropped_data, preprocessed_output_folder): super(ExperimentPlanner2D_v21, self).__init__(folder_with_cropped_data, preprocessed_output_folder) self.data_identifier = "nnUNetData_plans_v2.1_2D" self.plans_fname = join(self.preprocessed_output_folder, "nnUNetPlansv2.1_plans_2D.pkl") self.unet_base_num_features = 32 def get_properties_for_stage(self, current_spacing, original_spacing, original_shape, num_cases, num_modalities, num_classes): new_median_shape = np.round(original_spacing / current_spacing * original_shape).astype(int) dataset_num_voxels = np.prod(new_median_shape, dtype=np.int64) * num_cases input_patch_size = new_median_shape[1:] network_num_pool_per_axis, pool_op_kernel_sizes, conv_kernel_sizes, new_shp, \ shape_must_be_divisible_by = get_pool_and_conv_props(current_spacing[1:], input_patch_size, self.unet_featuremap_min_edge_length, self.unet_max_numpool) # we pretend to use 30 feature maps. This will yield the same configuration as in V1. The larger memory # footpring of 32 vs 30 is mor ethan offset by the fp16 training. We make fp16 training default # Reason for 32 vs 30 feature maps is that 32 is faster in fp16 training (because multiple of 8) ref = Generic_UNet.use_this_for_batch_size_computation_2D * Generic_UNet.DEFAULT_BATCH_SIZE_2D / 2 # for batch size 2 here = Generic_UNet.compute_approx_vram_consumption(new_shp, network_num_pool_per_axis, 30, self.unet_max_num_filters, num_modalities, num_classes, pool_op_kernel_sizes, conv_per_stage=self.conv_per_stage) while here > ref: axis_to_be_reduced = np.argsort(new_shp / new_median_shape[1:])[-1] tmp = deepcopy(new_shp) tmp[axis_to_be_reduced] -= shape_must_be_divisible_by[axis_to_be_reduced] _, _, _, _, shape_must_be_divisible_by_new = \ get_pool_and_conv_props(current_spacing[1:], tmp, self.unet_featuremap_min_edge_length, self.unet_max_numpool) new_shp[axis_to_be_reduced] -= shape_must_be_divisible_by_new[axis_to_be_reduced] # we have to recompute numpool now: network_num_pool_per_axis, pool_op_kernel_sizes, conv_kernel_sizes, new_shp, \ shape_must_be_divisible_by = get_pool_and_conv_props(current_spacing[1:], new_shp, self.unet_featuremap_min_edge_length, self.unet_max_numpool) here = Generic_UNet.compute_approx_vram_consumption(new_shp, network_num_pool_per_axis, self.unet_base_num_features, self.unet_max_num_filters, num_modalities, num_classes, pool_op_kernel_sizes, conv_per_stage=self.conv_per_stage) # print(new_shp) batch_size = int(np.floor(ref / here) * 2) input_patch_size = new_shp if batch_size < self.unet_min_batch_size: raise RuntimeError("This should not happen") # check if batch size is too large (more than 5 % of dataset) max_batch_size = np.round(self.batch_size_covers_max_percent_of_dataset * dataset_num_voxels / np.prod(input_patch_size, dtype=np.int64)).astype(int) batch_size = max(1, min(batch_size, max_batch_size)) plan = { 'batch_size': batch_size, 'num_pool_per_axis': network_num_pool_per_axis, 'patch_size': input_patch_size, 'median_patient_size_in_voxels': new_median_shape, 'current_spacing': current_spacing, 'original_spacing': original_spacing, 'pool_op_kernel_sizes': pool_op_kernel_sizes, 'conv_kernel_sizes': conv_kernel_sizes, 'do_dummy_2D_data_aug': False } return plan