import os
import fabio
import numpy as np
def generate_tiff_files(fn, path, prefix, compress):
"""
Generate tiff files from a hdf file.
:param fn, metadata, path, prefix:
:return: -
"""
print('Generating TIFF Files...')
with fabio.open(fn) as fabio_img:
# create_tiff(fabio_img.data, metadata, path, prefix, 1)
create_tiff(fabio_img, path, prefix, 1, compress)
if fabio_img.nframes > 1:
for i in range(2, fabio_img.nframes + 1):
fabio_img = fabio_img.next()
# create_tiff(fabio_img.data, metadata, path, prefix, i)
create_tiff(fabio_img, path, prefix, i, compress)
log_progress(i, fabio_img.nframes)
print('Completed')
generate_tiff_files(r'C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff\rat8_trabec1_225_data_000001.h5', r'rat8_trabec1_225_data_000001.h5', r'C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff', False)
这段程式码是我在这个网站上找到的, 他写说是可以把 h5转成tiff档. Convert HDF5 file to TIFF files — MuscleX 1.15.7 documentation
Source code在这: https://github.com/biocatiit/musclex/blob/master/musclex/utils/hdf5_to_tiffs.py
我尝试要把h5的档案转成tiff档,, 装了Fabio 的 package 后试着跑了第二段的程式码但却跑出下面的错误讯息, 尝试在stack overflow 上找过了可是大部分都说是因为档案受损导致,我用确定没受损的档案也照样会跑出错误讯息. 小弟我尝试用关键字找但还是不知道为什么fabio没办法读h5档, 我是这学期才刚开始学python, 还不是很熟悉. 请问我到底要怎么办才能让fabio正常读我想要的h5档?
错误讯息:
Generating TIFF Files...
Traceback (most recent call last):
File "C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff\hdf5_to_tiffs.py", line 120, in <module>
generate_tiff_files(r'C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff\rat8_trabec1_225_data_000001.h5', r'rat8_trabec1_225_data_000001.h5', r'C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff', False)
File "C:\Users\wayne\OneDrive\Desktop\Test_hdf5_to_tiff\hdf5_to_tiffs.py", line 51, in generate_tiff_files
with fabio.open(fn) as fabio_img:
File "C:\Users\wayne\AppData\Local\Programs\Python\Python310\lib\site-packages\fabio\openimage.py", line 180, in openimage
obj = obj.read(obj.filename, frame)
File "C:\Users\wayne\AppData\Local\Programs\Python\Python310\lib\site-packages\fabio\eigerimage.py", line 159, in read
self._data = self.dataset[0][self.currentframe,:,:]
File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "C:\Users\wayne\AppData\Local\Programs\Python\Python310\lib\site-packages\h5py\_hl\dataset.py", line 741, in __getitem__
return self._fast_reader.read(args)
File "h5py\_selector.pyx", line 370, in h5py._selector.Reader.read
OSError: Can't read data (can't open directory)