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# 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
import numpy as np
from nnunet.experiment_planning.common_utils import get_pool_and_conv_props_poolLateV2
from nnunet.experiment_planning.experiment_planner_baseline_3DUNet import ExperimentPlanner
from nnunet.network_architecture.generic_UNet import Generic_UNet
from nnunet.paths import *
class ExperimentPlannerAllConv3x3(ExperimentPlanner):
def __init__(self, folder_with_cropped_data, preprocessed_output_folder):
super(ExperimentPlannerAllConv3x3, self).__init__(folder_with_cropped_data, preprocessed_output_folder)
self.plans_fname = join(self.preprocessed_output_folder,
"nnUNetPlans" + "allConv3x3_plans_3D.pkl")
def get_properties_for_stage(self, current_spacing, original_spacing, original_shape, num_cases,
num_modalities, num_classes):
"""
Computation of input patch size starts out with the new median shape (in voxels) of a dataset. This is
opposed to prior experiments where I based it on the median size in mm. The rationale behind this is that
for some organ of interest the acquisition method will most likely be chosen such that the field of view and
voxel resolution go hand in hand to show the doctor what they need to see. This assumption may be violated
for some modalities with anisotropy (cine MRI) but we will have t live with that. In future experiments I
will try to 1) base input patch size match aspect ratio of input size in mm (instead of voxels) and 2) to
try to enforce that we see the same 'distance' in all directions (try to maintain equal size in mm of patch)
The patches created here attempt keep the aspect ratio of the new_median_shape
:param current_spacing:
:param original_spacing:
:param original_shape:
:param num_cases:
:return:
"""
new_median_shape = np.round(original_spacing / current_spacing * original_shape).astype(int)
dataset_num_voxels = np.prod(new_median_shape) * num_cases
# the next line is what we had before as a default. The patch size had the same aspect ratio as the median shape of a patient. We swapped t
# input_patch_size = new_median_shape
# compute how many voxels are one mm
input_patch_size = 1 / np.array(current_spacing)
# normalize voxels per mm
input_patch_size /= input_patch_size.mean()
# create an isotropic patch of size 512x512x512mm
input_patch_size *= 1 / min(input_patch_size) * 512 # to get a starting value
input_patch_size = np.round(input_patch_size).astype(int)
# clip it to the median shape of the dataset because patches larger then that make not much sense
input_patch_size = [min(i, j) for i, j in zip(input_patch_size, new_median_shape)]
network_num_pool_per_axis, pool_op_kernel_sizes, conv_kernel_sizes, new_shp, \
shape_must_be_divisible_by = get_pool_and_conv_props_poolLateV2(input_patch_size,
self.unet_featuremap_min_edge_length,
self.unet_max_numpool,
current_spacing)
ref = Generic_UNet.use_this_for_batch_size_computation_3D
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)
while here > ref:
axis_to_be_reduced = np.argsort(new_shp / new_median_shape)[-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_poolLateV2(tmp,
self.unet_featuremap_min_edge_length,
self.unet_max_numpool,
current_spacing)
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_poolLateV2(new_shp,
self.unet_featuremap_min_edge_length,
self.unet_max_numpool,
current_spacing)
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)
input_patch_size = new_shp
batch_size = Generic_UNet.DEFAULT_BATCH_SIZE_3D # This is what works with 128**3
batch_size = int(np.floor(max(ref / here, 1) * batch_size))
# check if batch size is too large
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)
max_batch_size = max(max_batch_size, self.unet_min_batch_size)
batch_size = max(1, min(batch_size, max_batch_size))
do_dummy_2D_data_aug = (max(input_patch_size) / input_patch_size[
0]) > self.anisotropy_threshold
for s in range(len(conv_kernel_sizes)):
conv_kernel_sizes[s] = [3 for _ in conv_kernel_sizes[s]]
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,
'do_dummy_2D_data_aug': do_dummy_2D_data_aug,
'pool_op_kernel_sizes': pool_op_kernel_sizes,
'conv_kernel_sizes': conv_kernel_sizes,
}
return plan
def run_preprocessing(self, num_threads):
pass
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