使用h5py创建的HDF5文件无法通过h5py打开 [英] HDF5 file created with h5py can't be opened by h5py

问题描述

我在Ubuntu 12.04（32位版本）下使用Anaconda作为Python发行版并在ipython笔记本中编写，显然创建了一个没有任何问题的HDF5文件。底层数据都是numpy数组。例如，

I created an HDF5 file apparently without any problems, under Ubuntu 12.04 (32bit version), using Anaconda as Python distribution and writing in ipython notebooks. The underlying data are all numpy arrays. For example,

import numpy as np
import h5py

f = h5py.File('myfile.hdf5','w')

group = f.create_group('a_group')

group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')

如果我尝试从新的iypthon笔记本打开此文件，但是，我收到一条错误消息：

If I try to open this file from a new iypthon notebook, though, I get an error message:

f = h5py.File('myfile.hdf5', "r")

---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
<ipython-input-4-b64ac5089cd4> in <module>()
----> 1 f = h5py.File(file_name, "r")

/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/files.pyc in __init__(self, name, mode, driver, libver, userblock_size, **kwds)
    220 
    221             fapl = make_fapl(driver, libver, **kwds)
--> 222             fid = make_fid(name, mode, userblock_size, fapl)
    223 
    224         Group.__init__(self, fid)

/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/files.pyc in make_fid(name, mode, userblock_size, fapl, fcpl)
     77 
     78     if mode == 'r':
---> 79         fid = h5f.open(name, h5f.ACC_RDONLY, fapl=fapl)
     80     elif mode == 'r+':
     81         fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

/home/sarah/anaconda/lib/python2.7/site-packages/h5py/h5f.so in h5py.h5f.open (h5py/h5f.c:1741)()

IOError: Unable to open file (Unable to find a valid file signature)

你能告诉我丢失的文件签名是什么吗？我在创建文件时是否遗漏了什么？

Can you tell me what that missing file signature is? Did I miss something when I created the file?

推荐答案

由于我们在对我的问题的评论中解决了这个问题，我是将结果写在这里以将其标记为已解决。

Since we resolved the issue in the comments on my question, I'm writing the results out here to mark it as solved.

主要问题是我在创建文件后忘记关闭文件。会有两个简单的选项：

The main problem was that I forgot to close the file after I created it. There would have been two simple options, either:

import numpy as np
import h5py

f = h5py.File('myfile.hdf5','w')
group = f.create_group('a_group')
group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')
f.close()

或者，我最喜欢的，因为文件自动关闭：

or, my favourite because the file is closed automatically:

import numpy as np
import h5py

with h5py.File('myfile.hdf5','w') as f:
    group = f.create_group('a_group')
    group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')

这篇关于使用h5py创建的HDF5文件无法通过h5py打开的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！