如何使用python将Hdf5文件部分复制到一个保持相同结构的新文件中? [英] How to partially copy using python an Hdf5 file into a new one keeping the same structure?

问题描述

我有一个很大的hdf5文件，看起来像这样:

I have a large hdf5 file that looks something like this:

A/B/dataset1, dataset2
A/C/dataset1, dataset2
A/D/dataset1, dataset2
A/E/dataset1, dataset2

...

我只想创建一个新文件: A/B/数据集1，数据集2 A/C/dataset1，dataset2

I want to create a new file with only that: A/B/dataset1, dataset2 A/C/dataset1, dataset2

在python中最简单的方法是什么?

What is the easiest way in python?

我做到了:

fs = h5py.File('source.h5', 'r')
fd = h5py.File('dest.h5', 'w')
fs.copy('group B', fd)

问题是我得到了dest.h5:

the problem is that I get for dest.h5:

B/dataset1, dataset2

并且我缺少部分乔木.

推荐答案

fs.copy('A/B', fd)不会将路径/A/B/复制到fd，它只会复制组B(如您所知！ ).因此，您首先需要创建路径的其余部分:

fs.copy('A/B', fd) doesn't copy the path /A/B/ into fd, it only copies the group B (as you've found out!). So you first need to create the rest of the path:

fd.create_group('A')
fs.copy('A/B', fd['/A'])

或者，如果您将经常使用该网上论坛:

or, if you will be using the group a lot:

fd_A = fd.create_group('A')
fs.copy('A/B', fd_A)

这会将组B从fs['/A/B']复制到fd['/A']:

In [1]: fd['A/B'].keys()
Out[1]: [u'dataset1', u'dataset2']

这是自动执行此操作的方法:

Here's an automatic way of doing this:

# Get the name of the parent for the group we want to copy
group_path = fs['/A/B'].parent.name

# Check that this group exists in the destination file; if it doesn't, create it
# This will create the parents too, if they don't exist
group_id = fd.require_group(group_path)

# Copy fs:/A/B/ to fd:/A/G
fs.copy('/A/B', group_id, name="G")

print(fd['/A/G'].keys())
# [u'dataset1', u'dataset2']

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