nnunet/preprocessing/cropping.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 SimpleITK as sitk
import numpy as np
import shutil
from batchgenerators.utilities.file_and_folder_operations import *
from multiprocessing import Pool
from collections import OrderedDict
import copy


def create_nonzero_mask(data):
    from scipy.ndimage import binary_fill_holes
    assert len(data.shape) == 4 or len(data.shape) == 3, "data must have shape (C, X, Y, Z) or shape (C, X, Y)"
    nonzero_mask = np.zeros(data.shape[1:], dtype=bool)
    for c in range(data.shape[0]):
        this_mask = data[c] != 0
        nonzero_mask = nonzero_mask | this_mask
    nonzero_mask = binary_fill_holes(nonzero_mask)
    return nonzero_mask


def get_bbox_from_mask(mask, outside_value=0):
    mask_voxel_coords = np.where(mask != outside_value)
    minzidx = int(np.min(mask_voxel_coords[0]))
    maxzidx = int(np.max(mask_voxel_coords[0])) + 1
    minxidx = int(np.min(mask_voxel_coords[1]))
    maxxidx = int(np.max(mask_voxel_coords[1])) + 1
    minyidx = int(np.min(mask_voxel_coords[2]))
    maxyidx = int(np.max(mask_voxel_coords[2])) + 1
    return [[minzidx, maxzidx], [minxidx, maxxidx], [minyidx, maxyidx]]


def crop_to_bbox(image, bbox):
    if len(image.shape) == 3:
        resizer = (slice(bbox[0][0], bbox[0][1]), slice(bbox[1][0], bbox[1][1]), slice(bbox[2][0], bbox[2][1]))
        return image[resizer]
    elif len(image.shape) == 2:
        resizer = (slice(bbox[1][0], bbox[1][1]), slice(bbox[2][0], bbox[2][1]))
        return image[resizer]


def get_case_identifier(case):
    case_identifier = case[0].split("/")[-1].split(".nii.gz")[0][:-5]
    return case_identifier


def get_case_identifier_from_npz(case):
    case_identifier = case.split("/")[-1][:-4]
    return case_identifier


def load_case_from_list_of_files(data_files, seg_file=None):
    assert isinstance(data_files, list) or isinstance(data_files, tuple), "case must be either a list or a tuple"
    properties = OrderedDict()
    data_itk = [sitk.ReadImage(f) for f in data_files]

    properties["original_size_of_raw_data"] = np.array(data_itk[0].GetSize())[[2, 1, 0]]
    properties["original_spacing"] = np.array(data_itk[0].GetSpacing())[[2, 1, 0]]
    properties["list_of_data_files"] = data_files
    properties["seg_file"] = seg_file

    properties["itk_origin"] = data_itk[0].GetOrigin()
    properties["itk_spacing"] = data_itk[0].GetSpacing()
    properties["itk_direction"] = data_itk[0].GetDirection()

    data_npy = np.vstack([sitk.GetArrayFromImage(d)[None] for d in data_itk])
    if seg_file is not None:

        seg_itk = sitk.ReadImage(seg_file)
        seg_npy = sitk.GetArrayFromImage(seg_itk)[None].astype(np.float32)
    else:
        seg_npy = None
    return data_npy.astype(np.float32), seg_npy, properties


def crop_to_nonzero(data, seg=None, nonzero_label=0):
    """

    :param data:
    :param seg:
    :param nonzero_label: this will be written into the segmentation map
    :return:
    """

    nonzero_mask = create_nonzero_mask(data)
    bbox = get_bbox_from_mask(nonzero_mask, 0)

    cropped_data = []
    for c in range(data.shape[0]):
        cropped = crop_to_bbox(data[c], bbox)
        cropped_data.append(cropped[None])
    data = np.vstack(cropped_data)


    if not isinstance(seg, type(None)):
        if seg.shape[1] == data.shape[1]:
            if seg is not None:
                cropped_seg = []
                for c in range(seg.shape[0]):
                    cropped = crop_to_bbox(seg[c], bbox)
                    cropped_seg.append(cropped[None])
                seg = np.vstack(cropped_seg)

            nonzero_mask = crop_to_bbox(nonzero_mask, bbox)[None]
            if seg is not None:
                seg[(seg == 0) & (nonzero_mask == 0)] = nonzero_label
            else:
                nonzero_mask = nonzero_mask.astype(int)
                nonzero_mask[nonzero_mask == 0] = nonzero_label
                nonzero_mask[nonzero_mask > 0] = 0
                seg = nonzero_mask
            return data, seg, bbox

        elif seg.shape[1] > data.shape[1]:
            # not very clean but should work
            bbox_for_seg = copy.copy(bbox)
            bbox_for_seg[0] = [0, seg.shape[1]]

            nonzero_mask_seg = np.array([nonzero_mask[0] for i in range(seg.shape[1])])
            if seg is not None:
                cropped_seg = []
                for c in range(seg.shape[0]):
                    cropped = crop_to_bbox(seg[c], bbox_for_seg)
                    cropped_seg.append(cropped[None])
                seg = np.vstack(cropped_seg)

            # dont understand what happens here\
            # all zeros values are set to -1. But why ?
            nonzero_mask = crop_to_bbox(nonzero_mask_seg, bbox_for_seg)[None]

            if seg is not None:
                seg[(seg == 0) & (nonzero_mask == 0)] = nonzero_label
            else:
                nonzero_mask = nonzero_mask.astype(int)
                nonzero_mask[nonzero_mask == 0] = nonzero_label
                nonzero_mask[nonzero_mask > 0] = 0
                seg = nonzero_mask
            return data, seg, bbox
    return data, seg, bbox


def get_patient_identifiers_from_cropped_files(folder):
    return [i.split("/")[-1][:-4] for i in subfiles(folder, join=True, suffix=".npz")]


class ImageCropper(object):
    def __init__(self, num_threads, output_folder=None):
        """
        This one finds a mask of nonzero elements (must be nonzero in all modalities) and crops the image to that mask.
        In the case of BRaTS and ISLES data this results in a significant reduction in image size
        :param num_threads:
        :param output_folder: whete to store the cropped data
        :param list_of_files:
        """
        self.output_folder = output_folder
        self.num_threads = num_threads

        if self.output_folder is not None:
            maybe_mkdir_p(self.output_folder)

    @staticmethod
    def crop(data, properties, seg=None):
        shape_before = data.shape
        data, seg, bbox = crop_to_nonzero(data, seg, nonzero_label=0)
        shape_after = data.shape
        print("before crop:", shape_before, "after crop:", shape_after, "spacing:",
              np.array(properties["original_spacing"]), "\n")

        properties["crop_bbox"] = bbox
        # TODO can only work with <50 segmentation classes in one label
        if not isinstance(seg, type(None)):
            classes = [np.unique(segx) for segx in seg[0]]
            for i,c in enumerate(classes):
                classes[i] = c if len(c)<50 else [0]
            properties["classes"] = classes
            seg[seg < -1] = 0
        properties["size_after_cropping"] = data[0].shape
        return data, seg, properties

    @staticmethod
    def crop_from_list_of_files(data_files, seg_file=None):
        data, seg, properties = load_case_from_list_of_files(data_files, seg_file)
        return ImageCropper.crop(data, properties, seg)

    def load_crop_save(self, case, case_identifier, overwrite_existing=False):
        try:
            print(case_identifier)
            if overwrite_existing \
                    or (not os.path.isfile(os.path.join(self.output_folder, "%s.npz" % case_identifier))
                        or not os.path.isfile(os.path.join(self.output_folder, "%s.pkl" % case_identifier))):
                data, seg, properties = self.crop_from_list_of_files(case[:-1], case[-1])

                all_data = np.vstack((data, seg.transpose((1, 0, 2, 3))))
                np.savez_compressed(os.path.join(self.output_folder, "%s.npz" % case_identifier), data=all_data)
                with open(os.path.join(self.output_folder, "%s.pkl" % case_identifier), 'wb') as f:
                    pickle.dump(properties, f)
        except Exception as e:
            print("Exception in", case_identifier, ":")
            print(e)
            raise e

    def get_list_of_cropped_files(self):
        return subfiles(self.output_folder, join=True, suffix=".npz")

    def get_patient_identifiers_from_cropped_files(self):
        return [i.split("/")[-1][:-4] for i in self.get_list_of_cropped_files()]

    def run_cropping(self, list_of_files, overwrite_existing=False, output_folder=None):
        """
        also copied ground truth nifti segmentation into the preprocessed folder so that we can use them for evaluation
        on the cluster
        :param list_of_files: list of list of files [[PATIENTID_TIMESTEP_0000.nii.gz], [PATIENTID_TIMESTEP_0000.nii.gz]]
        :param overwrite_existing:
        :param output_folder:
        :return:
        """
        if output_folder is not None:
            self.output_folder = output_folder

        output_folder_gt = os.path.join(self.output_folder, "gt_segmentations")
        maybe_mkdir_p(output_folder_gt)
        for j, case in enumerate(list_of_files):
            if case[-1] is not None:
                shutil.copy(case[-1], output_folder_gt)

        list_of_args = []
        for j, case in enumerate(list_of_files):
            case_identifier = get_case_identifier(case)
            # What the fuck happens here
            list_of_args.append((case, case_identifier, overwrite_existing))

        """
        self.load_crop_save(case, case_identifier)
        """
        p = Pool(self.num_threads)
        p.starmap(self.load_crop_save, list_of_args)
        p.close()
        p.join()


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

    def save_properties(self, case_identifier, properties):
        with open(os.path.join(self.output_folder, "%s.pkl" % case_identifier), 'wb') as f:
            pickle.dump(properties, f)