pandas 熊猫无法读取用 h5py 创建的 hdf5 文件
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Pandas can't read hdf5 file created with h5py
提问by Masha L.
I get pandas error when I try to read HDF5 format files that I have created with h5py. I wonder if I am just doing something wrong?
当我尝试读取我用 h5py 创建的 HDF5 格式文件时，我收到 pandas 错误。我想知道我是否只是做错了什么？
import h5py
import numpy as np
import pandas as pd
h5_file = h5py.File('test.h5', 'w')
h5_file.create_dataset('zeros', data=np.zeros(shape=(3, 5)), dtype='f')
h5_file.close()
pd_file = pd.read_hdf('test.h5', 'zeros')
gives an error: TypeError: cannot create a storer if the object is not existing nor a value are passed
给出错误：TypeError：如果对象不存在或传递值，则无法创建存储库
I tried to specify key set to '/zeros' (as I would do it with h5py when reading the file) with no luck.
我试图将键设置为“/zeros”（就像我在读取文件时使用 h5py 所做的那样）但没有运气。
If I use pandas.HDFStore to read it in, I get an empty store back:
如果我使用 pandas.HDFStore 来读取它，我会得到一个空的存储：
store = pd.HDFStore('test.h5')
>>> store
<class 'pandas.io.pytables.HDFStore'>
File path: test.h5
Empty
I have no troubles reading just created file back with h5py:
我用 h5py 读取刚刚创建的文件没有问题：
h5_back = h5py.File('test.h5', 'r')
h5_back['/zeros']
<HDF5 dataset "zeros": shape (3, 5), type "<f4">
Using these versions:
使用这些版本：
Python 3.4.3 (v3.4.3:9b73f1c3e601, Feb 23 2015, 02:52:03)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
pd.__version__
'0.16.2'
h5py.__version__
'2.5.0'
Many thanks in advance, Masha
提前非常感谢，玛莎
回答by Kevin S
I've worked a little on the pytablesmodule in pandas.ioand from what I know pandas interaction with HDF files is limited to specific structures that pandas understands. To see what these look like, you can try
我在pytables模块上做了一些工作，据pandas.io我所知，pandas 与 HDF 文件的交互仅限于pandas 理解的特定结构。要查看这些看起来像什么，您可以尝试
import pandas as pd
import numpy as np
pd.Series(np.zeros((3,5),dtype=np.float32).to_hdf('test.h5','test')
If you open 'test.h5' in HDFView, you will see a path /testwith 4 items that are needed to recreate the DataFrame.
如果您在HDFView 中打开“test.h5” ，您将看到一个/test包含 4 个项目的路径，这些项目需要重新创建DataFrame.
So I think your only option for reading in NumPy arrays is to read them in directly and then convert these to Pandas objects.
所以我认为读取 NumPy 数组的唯一选择是直接读取它们，然后将它们转换为 Pandas 对象。
