nnUNet数据格式一步到位准备

#导入必要的库
import os
from batchgenerators.utilities.file_and_folder_operations import save_json, subfiles
from typing import Tuple
import numpy as np

第一步：批量修改你每个文件夹内的文件名称，修改为nnunet能认识的文件名

#批量修改文件名称
folder_path = './TEST/'#影像存放文件夹
path_list=os.listdir(folder_path)#排序读取，负责会乱掉
num = 1
if __name__ == '__main__':
    for file in os.listdir(folder_path):
        s = '%03d' % num  # 前面补零占位,001,002,003....
        os.rename(os.path.join(folder_path, file), os.path.join(folder_path, 'pca_' + str(s) + '.nii.gz'))
        num += 1

修改完后就是这样子的 需要分别对训练测试和验证以及LABEL文件夹进行操作

第二部：生成相应的JSON文件

#获取文件夹内独立文件 
def get_identifiers_from_splitted_files(folder: str):
    uniques = np.unique([i[:-7] for i in subfiles(folder, suffix='.nii.gz', join=False)])
    return uniques
def generate_dataset_json(output_file: str, imagesTr_dir: str, imagesTs_dir: str, modalities: Tuple,
                          labels: dict, dataset_name: str, license: str = "Hebut AI", dataset_description: str = "",
                          dataset_reference="oai-zib", dataset_release='11/2021'):
    """
    :param output_file: This needs to be the full path to the dataset.json you intend to write, so
    output_file='DATASET_PATH/dataset.json' where the folder DATASET_PATH points to is the one with the
    imagesTr and labelsTr subfolders
    :param imagesTr_dir: path to the imagesTr folder of that dataset
    :param imagesTs_dir: path to the imagesTs folder of that dataset. Can be None
    :param modalities: tuple of strings with modality names. must be in the same order as the images (first entry
    corresponds to _0000.nii.gz, etc). Example: ('T1', 'T2', 'FLAIR').
    :param labels: dict with int->str (key->value) mapping the label IDs to label names. Note that 0 is always
    supposed to be background! Example: {0: 'background', 1: 'edema', 2: 'enhancing tumor'}
    :param dataset_name: The name of the dataset. Can be anything you want
    :param license:
    :param dataset_description:
    :param dataset_reference: website of the dataset, if available
    :param dataset_release:
    :return:
    """
     # 获取文件夹内各个独立的文件
    train_identifiers = get_identifiers_from_splitted_files(imagesTr_dir)
	# imagesTs_dir 文件夹可以为空，只要有训练的就行
    if imagesTs_dir is not None:
        test_identifiers = get_identifiers_from_splitted_files(imagesTs_dir)
    else:
        test_identifiers = []

    json_dict = {}
    json_dict['name'] = "PCA"
    json_dict['description'] = "PCA Segmentation"
    json_dict['tensorImageSize'] = "3D"
    json_dict['reference'] = dataset_reference
    json_dict['licence'] = license
    json_dict['release'] = dataset_release
    json_dict['modality'] = {"0": "MRI"}# 模态
    json_dict['labels'] = {
        "0": "background",
        "1": "XX"

    }
# 下面这些内容不需要更改
    json_dict['numTraining'] = len(train_identifiers)
    json_dict['numTest'] = len(test_identifiers)
    json_dict['training'] = [
        {'image': "./imagesTr/%s.nii.gz" % i, "label": "./labelsTr/%s.nii.gz" % i} for i
        in
        train_identifiers]
    json_dict['test'] = ["./imagesTs/%s.nii.gz" % i for i in test_identifiers]
	
    output_file += "dataset.json"
    if not output_file.endswith("dataset.json"):
        print("WARNING: output file name is not dataset.json! This may be intentional or not. You decide. "
              "Proceeding anyways...")
    save_json(json_dict, os.path.join(output_file))


if __name__ == "__main__":

    # 自行修改文件路径，当前在ubuntu环境下操作
    output_file = './'
    imagesTr_dir = './imagesTr/'
    imagesTs_dir = './imagesTs/'
    labelsTr = './labelsTr/'
    
    # 只需要给出空定义，具体内容在上面的函数中修改
    modalities = ''
    labels = {

    }
    get_identifiers_from_splitted_files(output_file)
    generate_dataset_json(output_file,
                          imagesTr_dir,
                          imagesTs_dir,
                          labelsTr,
                          modalities,
                          labels
                          )

搞定！

参考来源：

https://blog.csdn.net/See_Star/article/details/105910503
https://blog.csdn.net/qq_43210029/article/details/121350185?spm=1001.2014.3001.5502