nii转h5

#缺啥包直接pip install 即可
import matplotlib.pyplot as plt
import numpy as np
import os
import nibabel as nib
import h5py

path_image = '你原图像的路径'
path_label = '你标签的路径'
path_h5 = '存放h5文件的路径'

# 读取原始图像文件
def read_image(path):
    #print(path)
    images = nib.load(path).get_fdata().T
    return images
# 读取标签文件
def read_label(path):
    #print(path)
    labels = nib.load(path).get_fdata().T
    return labels

if __name__ == '__main__':

	#获取路径下的文件名
	imagelist = os.listdir(path_image)
    labellist = os.listdir(path_label)
    h5list = os.listdir(path_h5)
    
    #批量处理
    for idx in range(1, 100):
        images_name = '你原图像文件的名字{}.nii.gz'.format(idx)#.nii文件与.nii.gz语句相同
        labels_name = '你标签文件的名字{}.nii.gz'.format(idx) patient{}_heart.nii.gz
        hf_name = "你要的h5的文件名{}.h5".format(idx)        
        
        #
		if images_name not in imagelist:
            print(images_name+ " not exist! continue")
            continue
        if labels_name not in labellist:
            print(labels_name+ " not exist! continue")
            continue
        #防覆盖，需要修改已有的注释掉即可
        if hf_name in h5list:
            print(hf_name+' exist!')
            continue

        images_path = os.path.join(path_image, images_name)
        labels_path = os.path.join(path_label, labels_name)
        h5_save_path = os.path.join(path_h5, hf_name)

        images = read_image(images_path)
        labels = read_label(labels_path)

        # 写入h5文件
        with h5py.File(h5_save_path, mode='w') as hf:
            hf.create_dataset(name="images", dtype=float, data=images, compression="gzip")
            hf.create_dataset(name="labels", dtype=float, data=labels, compression="gzip")
        print("patient{} finished".format(idx))