nnunet/experiment_planning/experiment_planner_baseline_3DUNet.py

#    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.

import shutil
from collections import OrderedDict
from copy import deepcopy

import nnunet
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunet.configuration import default_num_threads
from nnunet.experiment_planning.DatasetAnalyzer import DatasetAnalyzer
from nnunet.experiment_planning.common_utils import get_pool_and_conv_props_poolLateV2
from nnunet.experiment_planning.utils import create_lists_from_splitted_dataset
from nnunet.network_architecture.generic_UNet import Generic_UNet
from nnunet.paths import *
from nnunet.preprocessing.cropping import get_case_identifier_from_npz
from nnunet.training.model_restore import recursive_find_python_class


class ExperimentPlanner(object):
    def __init__(self, folder_with_cropped_data, preprocessed_output_folder):
        self.folder_with_cropped_data = folder_with_cropped_data
        self.preprocessed_output_folder = preprocessed_output_folder
        self.list_of_cropped_npz_files = subfiles(self.folder_with_cropped_data, True, None, ".npz", True)

        self.preprocessor_name = "GenericPreprocessor"

        assert isfile(join(self.folder_with_cropped_data, "dataset_properties.pkl")), \
            "folder_with_cropped_data must contain dataset_properties.pkl"
        self.dataset_properties = load_pickle(join(self.folder_with_cropped_data, "dataset_properties.pkl"))

        self.plans_per_stage = OrderedDict()
        self.plans = OrderedDict()
        self.plans_fname = join(self.preprocessed_output_folder, "nnUNetPlans" + "fixed_plans_3D.pkl")
        self.data_identifier = default_data_identifier

        self.transpose_forward = [0, 1, 2]
        self.transpose_backward = [0, 1, 2]

        self.unet_base_num_features = Generic_UNet.BASE_NUM_FEATURES_3D
        self.unet_max_num_filters = 320
        self.unet_max_numpool = 999
        self.unet_min_batch_size = 2
        self.unet_featuremap_min_edge_length = 4

        self.target_spacing_percentile = 50
        self.anisotropy_threshold = 3
        self.how_much_of_a_patient_must_the_network_see_at_stage0 = 4  # 1/4 of a patient
        self.batch_size_covers_max_percent_of_dataset = 0.05  # all samples in the batch together cannot cover more
        # than 5% of the entire dataset

        self.conv_per_stage = 2

    def get_target_spacing(self):
        spacings = self.dataset_properties['all_spacings']

        # target = np.median(np.vstack(spacings), 0)
        # if target spacing is very anisotropic we may want to not downsample the axis with the worst spacing
        # uncomment after mystery task submission
        """worst_spacing_axis = np.argmax(target)
        if max(target) > (2.5 * min(target)):
            spacings_of_that_axis = np.vstack(spacings)[:, worst_spacing_axis]
            target_spacing_of_that_axis = np.percentile(spacings_of_that_axis, 5)
            target[worst_spacing_axis] = target_spacing_of_that_axis"""

        target = np.percentile(np.vstack(spacings), self.target_spacing_percentile, 0)
        return target

    def save_my_plans(self):
        with open(self.plans_fname, 'wb') as f:
            pickle.dump(self.plans, f)

    def load_my_plans(self):
        self.plans = load_pickle(self.plans_fname)

        self.plans_per_stage = self.plans['plans_per_stage']
        self.dataset_properties = self.plans['dataset_properties']

        self.transpose_forward = self.plans['transpose_forward']
        self.transpose_backward = self.plans['transpose_backward']

    def determine_postprocessing(self):
        pass
        """
        Spoiler: This is unused, postprocessing was removed. Ignore it.
        :return:
        print("determining postprocessing...")

        props_per_patient = self.dataset_properties['segmentation_props_per_patient']

        all_region_keys = [i for k in props_per_patient.keys() for i in props_per_patient[k]['only_one_region'].keys()]
        all_region_keys = list(set(all_region_keys))

        only_keep_largest_connected_component = OrderedDict()

        for r in all_region_keys:
            all_results = [props_per_patient[k]['only_one_region'][r] for k in props_per_patient.keys()]
            only_keep_largest_connected_component[tuple(r)] = all(all_results)

        print("Postprocessing: only_keep_largest_connected_component", only_keep_largest_connected_component)

        all_classes = self.dataset_properties['all_classes']
        classes = [i for i in all_classes if i > 0]

        props_per_patient = self.dataset_properties['segmentation_props_per_patient']

        min_size_per_class = OrderedDict()
        for c in classes:
            all_num_voxels = []
            for k in props_per_patient.keys():
                all_num_voxels.append(props_per_patient[k]['volume_per_class'][c])
            if len(all_num_voxels) > 0:
                min_size_per_class[c] = np.percentile(all_num_voxels, 1) * MIN_SIZE_PER_CLASS_FACTOR
            else:
                min_size_per_class[c] = np.inf

        min_region_size_per_class = OrderedDict()
        for c in classes:
            region_sizes = [l for k in props_per_patient for l in props_per_patient[k]['region_volume_per_class'][c]]
            if len(region_sizes) > 0:
                min_region_size_per_class[c] = min(region_sizes)
                # we don't need that line but better safe than sorry, right?
                min_region_size_per_class[c] = min(min_region_size_per_class[c], min_size_per_class[c])
            else:
                min_region_size_per_class[c] = 0

        print("Postprocessing: min_size_per_class", min_size_per_class)
        print("Postprocessing: min_region_size_per_class", min_region_size_per_class)
        return only_keep_largest_connected_component, min_size_per_class, min_region_size_per_class
        """

    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

        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 plan_experiment(self):
        use_nonzero_mask_for_normalization = self.determine_whether_to_use_mask_for_norm()
        print("Are we using the nonzero mask for normalizaion?", use_nonzero_mask_for_normalization)
        spacings = self.dataset_properties['all_spacings']
        sizes = self.dataset_properties['all_sizes']

        all_classes = self.dataset_properties['all_classes']
        modalities = self.dataset_properties['modalities']
        num_modalities = len(list(modalities.keys()))

        target_spacing = self.get_target_spacing()
        new_shapes = [np.array(i) / target_spacing * np.array(j) for i, j in zip(spacings, sizes)]

        max_spacing_axis = np.argmax(target_spacing)
        remaining_axes = [i for i in list(range(3)) if i != max_spacing_axis]
        self.transpose_forward = [max_spacing_axis] + remaining_axes
        self.transpose_backward = [np.argwhere(np.array(self.transpose_forward) == i)[0][0] for i in range(3)]

        # we base our calculations on the median shape of the datasets
        median_shape = np.median(np.vstack(new_shapes), 0)
        print("the median shape of the dataset is ", median_shape)

        max_shape = np.max(np.vstack(new_shapes), 0)
        print("the max shape in the dataset is ", max_shape)
        min_shape = np.min(np.vstack(new_shapes), 0)
        print("the min shape in the dataset is ", min_shape)

        print("we don't want feature maps smaller than ", self.unet_featuremap_min_edge_length, " in the bottleneck")

        # how many stages will the image pyramid have?
        self.plans_per_stage = list()

        target_spacing_transposed = np.array(target_spacing)[self.transpose_forward]
        median_shape_transposed = np.array(median_shape)[self.transpose_forward]
        print("the transposed median shape of the dataset is ", median_shape_transposed)

        print("generating configuration for 3d_fullres")
        self.plans_per_stage.append(self.get_properties_for_stage(target_spacing_transposed, target_spacing_transposed,
                                                                  median_shape_transposed,
                                                                  len(self.list_of_cropped_npz_files),
                                                                  num_modalities, len(all_classes) + 1))

        # thanks Zakiyi (https://github.com/MIC-DKFZ/nnUNet/issues/61) for spotting this bug :-)
        # if np.prod(self.plans_per_stage[-1]['median_patient_size_in_voxels'], dtype=np.int64) / \
        #        architecture_input_voxels < HOW_MUCH_OF_A_PATIENT_MUST_THE_NETWORK_SEE_AT_STAGE0:
        architecture_input_voxels_here = np.prod(self.plans_per_stage[-1]['patch_size'], dtype=np.int64)
        if np.prod(median_shape) / architecture_input_voxels_here < \
                self.how_much_of_a_patient_must_the_network_see_at_stage0:
            more = False
        else:
            more = True

        if more:
            print("generating configuration for 3d_lowres")
            # if we are doing more than one stage then we want the lowest stage to have exactly
            # HOW_MUCH_OF_A_PATIENT_MUST_THE_NETWORK_SEE_AT_STAGE0 (this is 4 by default so the number of voxels in the
            # median shape of the lowest stage must be 4 times as much as the network can process at once (128x128x128 by
            # default). Problem is that we are downsampling higher resolution axes before we start downsampling the
            # out-of-plane axis. We could probably/maybe do this analytically but I am lazy, so here
            # we do it the dumb way

            lowres_stage_spacing = deepcopy(target_spacing)
            num_voxels = np.prod(median_shape, dtype=np.float64)
            while num_voxels > self.how_much_of_a_patient_must_the_network_see_at_stage0 * architecture_input_voxels_here:
                max_spacing = max(lowres_stage_spacing)
                if np.any((max_spacing / lowres_stage_spacing) > 2):
                    lowres_stage_spacing[(max_spacing / lowres_stage_spacing) > 2] \
                        *= 1.01
                else:
                    lowres_stage_spacing *= 1.01
                num_voxels = np.prod(target_spacing / lowres_stage_spacing * median_shape, dtype=np.float64)

                lowres_stage_spacing_transposed = np.array(lowres_stage_spacing)[self.transpose_forward]
                new = self.get_properties_for_stage(lowres_stage_spacing_transposed, target_spacing_transposed,
                                                    median_shape_transposed,
                                                    len(self.list_of_cropped_npz_files),
                                                    num_modalities, len(all_classes) + 1)
                architecture_input_voxels_here = np.prod(new['patch_size'], dtype=np.int64)
            if 2 * np.prod(new['median_patient_size_in_voxels'], dtype=np.int64) < np.prod(
                    self.plans_per_stage[0]['median_patient_size_in_voxels'], dtype=np.int64):
                self.plans_per_stage.append(new)

        self.plans_per_stage = self.plans_per_stage[::-1]
        self.plans_per_stage = {i: self.plans_per_stage[i] for i in range(len(self.plans_per_stage))}  # convert to dict

        print(self.plans_per_stage)
        print("transpose forward", self.transpose_forward)
        print("transpose backward", self.transpose_backward)

        normalization_schemes = self.determine_normalization_scheme()
        only_keep_largest_connected_component, min_size_per_class, min_region_size_per_class = None, None, None
        # removed training data based postprocessing. This is deprecated

        # these are independent of the stage
        plans = {'num_stages': len(list(self.plans_per_stage.keys())), 'num_modalities': num_modalities,
                 'modalities': modalities, 'normalization_schemes': normalization_schemes,
                 'dataset_properties': self.dataset_properties, 'list_of_npz_files': self.list_of_cropped_npz_files,
                 'original_spacings': spacings, 'original_sizes': sizes,
                 'preprocessed_data_folder': self.preprocessed_output_folder, 'num_classes': len(all_classes),
                 'all_classes': all_classes, 'base_num_features': self.unet_base_num_features,
                 'use_mask_for_norm': use_nonzero_mask_for_normalization,
                 'keep_only_largest_region': only_keep_largest_connected_component,
                 'min_region_size_per_class': min_region_size_per_class, 'min_size_per_class': min_size_per_class,
                 'transpose_forward': self.transpose_forward, 'transpose_backward': self.transpose_backward,
                 'data_identifier': self.data_identifier, 'plans_per_stage': self.plans_per_stage,
                 'preprocessor_name': self.preprocessor_name,
                 'conv_per_stage': self.conv_per_stage,
                 }

        self.plans = plans
        self.save_my_plans()

    def determine_normalization_scheme(self):
        schemes = OrderedDict()
        modalities = self.dataset_properties['modalities']
        num_modalities = len(list(modalities.keys()))

        for i in range(num_modalities):
            if modalities[i] == "CT" or modalities[i] == 'ct':
                schemes[i] = "CT"
            elif modalities[i] == 'noNorm':
                schemes[i] = "noNorm"
            else:
                schemes[i] = "nonCT"
        return schemes

    def save_properties_of_cropped(self, case_identifier, properties):
        with open(join(self.folder_with_cropped_data, "%s.pkl" % case_identifier), 'wb') as f:
            pickle.dump(properties, f)

    def load_properties_of_cropped(self, case_identifier):
        with open(join(self.folder_with_cropped_data, "%s.pkl" % case_identifier), 'rb') as f:
            properties = pickle.load(f)
        return properties

    def determine_whether_to_use_mask_for_norm(self):
        # only use the nonzero mask for normalization of the cropping based on it resulted in a decrease in
        # image size (this is an indication that the data is something like brats/isles and then we want to
        # normalize in the brain region only)
        modalities = self.dataset_properties['modalities']
        num_modalities = len(list(modalities.keys()))
        use_nonzero_mask_for_norm = OrderedDict()

        for i in range(num_modalities):
            if "CT" in modalities[i]:
                use_nonzero_mask_for_norm[i] = False
            else:
                all_size_reductions = []
                for k in self.dataset_properties['size_reductions'].keys():
                    all_size_reductions.append(self.dataset_properties['size_reductions'][k])

                if np.median(all_size_reductions) < 3 / 4.:
                    print("using nonzero mask for normalization")
                    use_nonzero_mask_for_norm[i] = True
                else:
                    print("not using nonzero mask for normalization")
                    use_nonzero_mask_for_norm[i] = False

        for c in self.list_of_cropped_npz_files:
            case_identifier = get_case_identifier_from_npz(c)
            properties = self.load_properties_of_cropped(case_identifier)
            properties['use_nonzero_mask_for_norm'] = use_nonzero_mask_for_norm
            self.save_properties_of_cropped(case_identifier, properties)
        use_nonzero_mask_for_normalization = use_nonzero_mask_for_norm
        return use_nonzero_mask_for_normalization

    def write_normalization_scheme_to_patients(self):
        """
        This is used for test set preprocessing
        :return: 
        """
        for c in self.list_of_cropped_npz_files:
            case_identifier = get_case_identifier_from_npz(c)
            properties = self.load_properties_of_cropped(case_identifier)
            properties['use_nonzero_mask_for_norm'] = self.plans['use_mask_for_norm']
            self.save_properties_of_cropped(case_identifier, properties)

    def run_preprocessing(self, num_threads):
        if os.path.isdir(join(self.preprocessed_output_folder, "gt_segmentations")):
            shutil.rmtree(join(self.preprocessed_output_folder, "gt_segmentations"))
        shutil.copytree(join(self.folder_with_cropped_data, "gt_segmentations"),
                        join(self.preprocessed_output_folder, "gt_segmentations"))
        normalization_schemes = self.plans['normalization_schemes']
        use_nonzero_mask_for_normalization = self.plans['use_mask_for_norm']
        intensityproperties = self.plans['dataset_properties']['intensityproperties']
        preprocessor_class = recursive_find_python_class([join(nnunet.__path__[0], "preprocessing")],
                                                         self.preprocessor_name, current_module="nnunet.preprocessing")
        assert preprocessor_class is not None
        preprocessor = preprocessor_class(normalization_schemes, use_nonzero_mask_for_normalization,
                                         self.transpose_forward,
                                          intensityproperties)
        target_spacings = [i["current_spacing"] for i in self.plans_per_stage.values()]
        if self.plans['num_stages'] > 1 and not isinstance(num_threads, (list, tuple)):
            num_threads = (default_num_threads, num_threads)
        elif self.plans['num_stages'] == 1 and isinstance(num_threads, (list, tuple)):
            num_threads = num_threads[-1]
        preprocessor.run(target_spacings, self.folder_with_cropped_data, self.preprocessed_output_folder,
                         self.plans['data_identifier'], num_threads)


if __name__ == "__main__":
    import argparse

    parser = argparse.ArgumentParser()
    parser.add_argument("-t", "--task_ids", nargs="+", help="list of int")
    parser.add_argument("-p", action="store_true", help="set this if you actually want to run the preprocessing. If "
                                                        "this is not set then this script will only create the plans file")
    parser.add_argument("-tl", type=int, required=False, default=8, help="num_threads_lowres")
    parser.add_argument("-tf", type=int, required=False, default=8, help="num_threads_fullres")

    args = parser.parse_args()
    task_ids = args.task_ids
    run_preprocessing = args.p
    tl = args.tl
    tf = args.tf

    tasks = []
    for i in task_ids:
        i = int(i)
        candidates = subdirs(nnUNet_cropped_data, prefix="Task%03.0d" % i, join=False)
        assert len(candidates) == 1
        tasks.append(candidates[0])

    for t in tasks:
        try:
            print("\n\n\n", t)
            cropped_out_dir = os.path.join(nnUNet_cropped_data, t)
            preprocessing_output_dir_this_task = os.path.join(preprocessing_output_dir, t)
            splitted_4d_output_dir_task = os.path.join(nnUNet_raw_data, t)
            lists, modalities = create_lists_from_splitted_dataset(splitted_4d_output_dir_task)

            dataset_analyzer = DatasetAnalyzer(cropped_out_dir, overwrite=False)
            _ = dataset_analyzer.analyze_dataset()  # this will write output files that will be used by the ExperimentPlanner

            maybe_mkdir_p(preprocessing_output_dir_this_task)
            shutil.copy(join(cropped_out_dir, "dataset_properties.pkl"), preprocessing_output_dir_this_task)
            shutil.copy(join(nnUNet_raw_data, t, "dataset.json"), preprocessing_output_dir_this_task)

            threads = (tl, tf)

            print("number of threads: ", threads, "\n")

            exp_planner = ExperimentPlanner(cropped_out_dir, preprocessing_output_dir_this_task)
            exp_planner.plan_experiment()
            if run_preprocessing:
                exp_planner.run_preprocessing(threads)
        except Exception as e:
            print(e)