首先先查看一下.h5文件中的内容:
import h5py
def show_hdf5_datasets(h5_file_path):
with h5py.File(h5_file_path, 'r') as h5_file:
print("Datasets in the HDF5 file:")
for dataset_name in h5_file:
print(dataset_name)
h5_file_path = 'input_file.h5'
show_hdf5_datasets(h5_file_path)
然后根据里面内容进行对应的转换:
以我自己的为例:我里面是 image 和 label 两个内容,所以我的转换如下(其他都是类似,大家类比一下):
import h5py
import numpy as np
import nibabel as nib
def h5_to_nifti(h5_file_path, nifti_file_path, nifti_label_file_path):
# 读取HDF5文件
with h5py.File(h5_file_path, 'r') as h5_file:
# 获取'image'和'label'数据集
if 'image' not in h5_file:
raise ValueError("HDF5 file should contain a dataset named 'image'")
if 'label' not in h5_file:
raise ValueError("HDF5 file should contain a dataset named 'label'")
image_data = h5_file['image'][:]
label_data = h5_file['label'][:]
# 转换为NIfTI格式
#
image_data = np.transpose(image_data, (2, 1, 0))
label_data = np.transpose(label_data, (2, 1, 0))
# 创建NIfTI图像对象
nifti_img = nib.Nifti1Image(image_data, affine=np.eye(4))
nifti_label_img = nib.Nifti1Image(label_data, affine=np.eye(4))
# 保存为NIfTI文件
nib.save(nifti_img, nifti_file_path)
nib.save(nifti_label_img, nifti_label_file_path)
h5_file_path = 'input_file.h5'
nifti_file_path = 'output_image.nii.gz'
nifti_label_file_path = 'output_label.nii.gz'
h5_to_nifti(h5_file_path, nifti_file_path, nifti_label_file_path)